NOGO Receptor-Mediated Blockade of Axonal Growth

ABSTRACT

Disclosed are NgR proteins and biologically active Nogo (ligand) protein fragments. Also disclosed are compositions and methods for modulating the expression or activity of the Nogo and NgR protein. Also disclosed are peptides which block Nogo-mediated inhibition of axonal extension. The compositions and methods of the invention are useful in the treatment of cranial or cerebral trauma, spinal cord injury, stroke or a demyelinating disease.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. application Ser. No.14/088,158, filed Nov. 22, 2013, which is a divisional U.S. applicationSer. No. 13/788,923, filed Mar. 7, 2013, now abandoned, which is adivisional of U.S. application Ser. No. 12/693,940, filed Jan. 26, 2010,now U.S. Pat. No. 8,394,929, which is a divisional of U.S. applicationSer. No. 11/516,024, filed Sep. 6, 2006, now abandoned, which is adivisional of U.S. application Ser. No. 09/972,599, filed Oct. 6, 2001,now U.S. Pat. No. 7,119,165, which is a continuation-in-part of U.S.application Ser. No. 09/758,140, filed Jan. 12, 2001, now abandoned,which claims benefit under 35 U.S.C. §119(e) to U.S. ProvisionalApplication No. 60/175,707, filed Jan. 12, 2000; U.S. ProvisionalApplication No. 60/207,366, filed May 26, 2000; and U.S. ProvisionalApplication No. 60/236,378, filed Sep. 29, 2000, which are hereinincorporated by reference in their entireties. U.S. application Ser. No.09/972,599 is also a continuation-in-part of international applicationPCT/US01/01041, filed Jan. 12, 2001.

U.S. GOVERNMENT SUPPORT

This invention was made with government support under RO1-NS 33020,RO1-NS39962 and RO1-NS42304 awarded by National Institutes of Health.The government has certain rights in the invention.

REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY

The content of the electronically submitted sequence listing in ASCIItext file (2681.041000A_SL.txt; Size: 69,579 bytes; and Date ofCreation: Jun. 29, 2015) filed with the application is incorporatedherein by reference in its entirety.

FIELD OF THE INVENTION

The invention relates to neurology and molecular biology. Moreparticularly, the invention relates to CNS neurons and axonal growth

BACKGROUND OF THE INVENTION

Axons and dendrites of neurons are long cellular extensions fromneurons. At the distal tip of an extending axon or neurite is aspecialized region, known as the growth cone. Growth cones areresponsible for sensing the local environment and moving toward theneuron's target cell. Growth cones are hand shaped, with several longfilopodia that differentially adhere to surfaces in the embryo. Growthcones can be sensitive to several guidance cues, for example, surfaceadhesiveness, growth factors, neurotransmitters and electric fields. Theguidance of growth at the cone depends on various classes of adhesionmolecules, intercellular signals, as well as factors which stimulate andinhibit growth cones. The growth cone located at the end of a growingneurite advances at various rates, but typically at the speed of one totwo millimeters per day. The cone consists of a broad and flatexpansion, with numerous long microspikes or filopodia that extend likespikes. These filopodia are continually active. While some filopodiaretract back into the growth cone, others continue to elongate throughthe substratum. The elongations between different filopodia formlamellipodia.

The growth cone can explore the area that is ahead of it and on eitherside with its lamellipodia and filopodia. When an elongation comes incontact with a surface that is unfavorable, it withdraws. When anelongation comes into contact with a favorable surface, it continues toextend and can manipulate the growth cone moving in that direction.Hence, the growth cone can be guided by small variations in surfaceproperties of the substrata. When the growth cone reaches an appropriatetarget cell a synaptic connection is created.

Damaged neurons do not regenerate in the central nervous system (CNS)following injury due to trauma and disease. The absence of axonregeneration following injury can be attributed to the presence of axongrowth inhibitors. These inhibitors are predominantly associated withmyelin and constitute an important barrier to regeneration. Axon growthinhibitors are present in CNS-derived myelin and the plasma membrane ofoligodendrocytes, which synthesize myelin in the CNS (Schwab et al.,(1993) Ann. Rev. Neurosci. 16, 565-595).

CNS myelin is an elaborate extension of the oligodendrocyte cellmembrane. A single oligodendrocyte myelinates as many as thirtydifferent CNS axonal segments. Oligodendrocyte membrane extensions wraparound the axons in a concentric fashion to form the myelin sheath.Tightly compacted mature myelin consists of parallel layers ofbimolecular lipids apposed to layers of hydrated protein. Active myelinsynthesis starts in utero and continues for the first two years of humanlife. Slower synthesis continues through childhood and adolescence whileturnover of mature myelin continues at a slower rate throughout adultlife. Both developing and mature forms of myelin are susceptible toinjury from disease or physical trauma resulting in degradation of themyelin surrounding axons.

Myelin-associated inhibitors appear to be a primary contributor to thefailure of CNS axon regeneration in vivo after an interruption of axonalcontinuity, while other non-myelin associated axon growth inhibitors inthe CNS may play a lesser role. These inhibitors block axonalregeneration following neuronal injury due to trauma, stroke, or viralinfection.

Numerous myelin-derived axon growth inhibitors have been characterized(see, for review, David et al., (1999) WO9953945; Bandman et al., (1999)U.S. Pat. No. 5,858,708; Schwab, (1996) Neurochem. Res. 21, 755-761).Several components of CNS white matter, NI35, NI250 (Nogo) andMyelin-associated glycoprotein (MAG), which have inhibitory activity foraxonal extension, have been also been described (Schwab et al., (1990)WO9005191; Schwab et al., (1997) U.S. Pat. No. 5,684,133). Inparticular, Nogo is a 250 kDa myelin-associated axon growth inhibitorwhich has been cloned and characterized (Nagase et al., (1998) DNA Res.5, 355-364; Schwab, (1990) Exp. Neurol. 109, 2-5). The Nogo cDNA wasfirst identified through random analysis of brain cDNA and had nosuggested function (Nagase et al., (1998) DNA Res. 5, 355-364).

Schwab and colleagues published the sequence of six peptides randomlyderived from a proteolytic digest of presumed bovine NI250 (Nogo)protein (Spillmann et al., (1998) J. Biol. Chem. 273, 19283-19293). Aprobable full-length cDNA sequence for this protein was recentlydeposited in the GenBank. This 4.1 kilobase human cDNA clone, KIAA0886,is derived from the Kazusa DNA Research Institute effort to sequencerandom high molecular weight brain-derived cDNA (Nagase et al., (1998)DNA Res. 31, 355-364). This novel cDNA clone encodes a 135 kDa proteinthat includes all six of the peptide sequences derived from bovine Nogo.

The human Nogo-A sequence shares high homology over its carboxyl thirdwith the Reticulon (Rtn) protein family. Rtn1 has also been termedneuro-endocrine specific protein (NSP) because it is expressedexclusively in neuro-endocrine cells (Van de Velde et al., (1994) J.Cell. Sci. 107, 2403-2416). All Rtn proteins share a 200 amino acidresidue region of sequence similarity at the carboxyl terminus of theprotein (Van de Velde et al., (1994) J. Cell. Sci. 107, 2403-2416;Roebroek et al., (1996) Genomics 32, 191-199; Roebroek et al., (1998)Genomics 51, 98-106; Moreira et al., (1999) Genomics 58, 73-81; Morriset al., (1991) Biochim. Biophys. Acta 1450, 68-76). Related sequenceshave been recognized in the fly and worm genomes (Moreira et al., (1999)Genomics 58, 73-81). This region is approximately 70% identical acrossthe Rtn family. Amino terminal regions are not related to one anotherand are derived from various alternative RNA splicing events.

From analysis of sequences deposited in the GenBank and by homology withpublished Rtn1 isoforms, three forms of the Nogo protein are predicted(Nogo-A, Nogo-B, Nogo-C). Nogo-B of 37 kDa might possibly correspond toN135, and explain the antigenic relatedness of the N135 and N1250(Nogo-A) axon outgrowth inhibiting activity. Nogo-C-Myc exhibits anelectrophoretic mobility of 25 kDa by SDS-PAGE and has been describedpreviously as Rtn4 and vp2015. The ability of Nogo-A protein to inhibitaxonal regeneration has been recognized only recently (GrandPré et al.,(2000) Nature 403, 439-444; Chen et al., (2000) Nature 403, 434-439;Prinjha et al., (2000) Nature 403, 483-484).

The absence of re-extension of axons across lesions in the CNS followinginjury has been attributed as a cause of the permanent deleteriouseffects associated with trauma, stroke and demyelinating disorders.Modulation of N1250 has been described as a means for treatment ofregeneration for neurons damaged by trauma, infarction and degenerativedisorders of the CNS (Schwab et al., (1994) WO9417831; Tatagiba et al.,(1997) Neurosurgery 40, 541-546) as well as malignant tumors in the CNSsuch as glioblastoma (Schwab et al., (1993) U.S. Pat. No. 5,250,414;Schwab et al., (2000) U.S. Pat. No. 6,025,333).

Antibodies which recognize N1250 have been reported to be useful in thediagnosis and treatment of nerve damage resulting from trauma,infarction and degenerative disorders of the CNS (Schnell & Schwab,(1990) Nature 343, 269-272; Schwab et al., (1997) U.S. Pat. No.5,684,133). In axons which become myelinated, there is a correlationwith the development of myelin and the appearance of Nogo. After Nogo isblocked by antibodies, neurons can again extend across lesions caused bynerve damage (Varga et al., (1995) Proc. Natl. Acad. Sci. USA 92,10959-10963).

The mechanism of action whereby Nogo inhibits axonal growth has not yetbeen elucidated. Identification and characterization of this mechanismof action and the biochemical pathways associated with the effects ofNogo would be useful in treatment of disease states associated withaxonal injury and axonal demyelination.

SUMMARY OF THE INVENTION

The present invention is based on the discovery of Nogo receptorproteins and biologically active Nogo protein (ligand) fragments. Theinvention provides an isolated nucleic acid molecule selected from thegroup consisting of an isolated nucleic acid molecule that encodes theamino acid sequence of SEQ ID NO: 2, 4, 8, 10, 12, 14, 16, 18 or 20; anisolated nucleic acid molecule that encodes a fragment of at least six,e.g., ten, fifteen, twenty, twenty-five, thirty, forty, fifty, sixty orseventy amino acids of SEQ ID NO: 2, 4, 8, 10, 12, 14, 16, 18 or 20; anisolated nucleic acid molecule which hybridizes to a nucleic acidmolecule comprising the complement of SEQ ID NO: 1, 3, 7, 9, 11, 13, 15,17 or 19 under high stringency conditions; and an isolated nucleic acidmolecule with at least seventy-five, e.g., eighty, eighty-five, ninetyor ninety-five percent amino acid sequence identity to SEQ ID NO: 1, 3,7, 9, 11, 13, 15, 17 or 19. In a preferred embodiment, the inventionincludes an isolated nucleic acid molecule comprising nucleotides 166 to1584 of SEQ ID NO: 1 or nucleotides 178 to 1596 of SEQ ID NO: 3.

The present invention further includes the nucleic acid moleculesoperably linked to one or more expression control elements, includingvectors comprising the isolated nucleic acid molecules. The inventionfurther includes host cells transformed to contain the nucleic acidmolecules of the invention and methods for producing a proteincomprising the step of culturing a host cell transformed with a nucleicacid molecule of the invention under conditions in which the protein isexpressed.

The present invention includes an isolated polypeptide selected from thegroup consisting of an isolated polypeptide comprising the amino acidsequence of SEQ ID NO: 2, 4, 8, 10, 12, 14, 16, 18 or 20; an isolatedpolypeptide comprising a fragment of at least six, e.g., ten, fifteen,twenty, twenty-five, thirty, forty, fifty, sixty or seventy amino acidsof SEQ ID NO: 2, 4, 8, 10, 12, 14, 16, 18 or 20; an isolated polypeptidecomprising the amino acid sequence of SEQ ID NO: 2, 4, 8, 10, 12, 14,16, 18 or 20 comprising at least one, e.g., five, ten, fifteen or twentyconservative amino acid substitutions; an isolated polypeptidecomprising the amino acid sequence of SEQ ID NO: 2, 4, 8, 10, 12, 14,16, 18 or 20 comprising one, e.g., five, ten, fifteen or twentynaturally occurring amino acid sequence substitutions; and an isolatedpolypeptide with at least seventy-five, e.g., eighty, eighty-five,ninety or ninety-five percent amino acid sequence identity to SEQ ID NO:2, 4, 8, 10, 12, 14, 16, 18 or 20. The invention also includes chimericpolypeptides comprising the amino acid sequence of SEQ ID NO: 2, 4, 8,10, 12, 14, 16, 18 or 20.

The invention further provides antibodies that bind to a Nogo proteinand antibodies which bind to a Nogo receptor protein. The antibodies canbe monoclonal or polyclonal antibodies. In addition, the antibody may behumanized. The invention also includes antibody fragments which displayantigen binding activity.

The invention includes a method of identifying an agent which modulatesNogo protein or Nogo receptor protein expression comprising the steps ofproviding a cell expressing a Nogo protein or Nogo receptor protein;contacting the cell with a candidate agent; and detecting an increase ordecrease in the level of Nogo protein or Nogo receptor proteinexpression in the presence of the candidate agent relative to the levelof Nogo protein or Nogo receptor protein expression in the absence ofthe candidate agent.

The invention also includes a method of identifying an agent whichmodulates at least one activity of a Nogo protein or Nogo receptorprotein comprising the steps of providing a cell expressing a Nogoprotein or Nogo receptor protein; contacting the cell with a candidateagent; and detecting an increase or decrease in the level of Nogoprotein or Nogo receptor protein activity in the presence of thecandidate agent relative to the level of Nogo protein or Nogo receptorprotein activity in the absence of the candidate agent. In oneembodiment of the invention, the activity is growth cone movement. Inanother embodiment, the agent is selected from the group consisting of aNogo protein fragment, anti-Nogo antibody and anti-Nogo receptorantibody.

The invention further includes a method of identifying a binding partnerfor a Nogo receptor protein comprising the steps of providing a Nogoreceptor protein; contacting the Nogo receptor with a candidate bindingpartner; and detecting binding of the candidate binding partner to theNogo receptor protein. In one embodiment, the binding partner isselected from the group consisting of a Nogo protein fragment, ananti-Nogo antibody, an anti-Nogo receptor antibody fragment; and ahumanized anti-Nogo receptor antibody.

The invention encompasses a method of treating a central nervous systemdisorder in a mammal comprising the step of administering an effectiveamount of an agent which modulates the expression of a Nogo protein orNogo receptor protein. In some embodiments of the invention theexpression is decreased, while in other embodiments, it is increased.

The invention further encompasses a method of treating a central nervoussystem disorder in a mammal comprising the step of administering aneffective amount of an agent which modulates the activity of a Nogoprotein or Nogo receptor protein. The activity may be either increasedor decreased. If the activity is decreased, the agent can be e.g., apolypeptide comprising the amino acid sequence of SEQ ID NO: 8, 10, 12,18 or 20; a full length Nogo receptor protein; a Nogo receptor proteinfragment; a soluble Nogo receptor protein fragment; or an anti-Nogoreceptor antibody or active fragment thereof. If the activity isincreased the agent is a polypeptide selected from the group consistingof SEQ ID NO: 14 and 16.

A soluble Nogo receptor protein can comprise a fragment of at least six,e.g., ten, fifteen, twenty, twenty-five, thirty, forty, fifty, sixty orseventy amino acids of SEQ ID NO: 2 or 4; the amino acid sequence of SEQID NO: 2, 4, 8, 10, 12, 14, 16, 18 or 20; the amino acid sequence of SEQID NO: 2, 4, 8, 10, 12, 14, 16, 18 or 20 comprising at least one, e.g.,five, ten, fifteen or twenty conservative amino acid substitutions; theamino acid sequence of SEQ ID NO: 2, 4, 8, 10, 12, 14, 16, 18 or 20comprising one, e.g., five, ten, fifteen or twenty naturally occurringamino acid sequence substitutions.

In some embodiments, the central nervous system disorder is a result ofcranial or cerebral trauma, spinal cord injury, stroke or ademyelinating disease. Examples of demyelinating diseases are multiplesclerosis, monophasic demyelination, encephalomyelitis, multifocalleukoencephalopathy, panencephalitis, Marchiafava-Bignami disease,pontine myelinolysis, adrenoleukodystrophy, Pelizaeus-Merzbacherdisease, Spongy degeneration, Alexander's disease, Canavan's disease,metachromatic leukodystrophy and Krabbe's disease.

The invention further encompasses an isolated peptide that specificallybinds to a Nogo receptor protein. The specific binding of the peptide tothe Nogo receptor protein preferably has at least one of the followingeffects: inhibition of binding of a Nogo protein to the Nogo receptorprotein, blockade of Nogo-mediated inhibition of axonal growth,modulation of Nogo protein expression, or modulation of Nogo receptorprotein expression. In some embodiments, the isolated peptide comprisesthe amino acid sequence of SEQ ID NO: 8, 10, 12, 14, 16, 18 or 20, orone of the foregoing with one or more, e.g., five, ten, fifteen ortwenty consecutive amino acid substitutions or naturally occurring aminoacid substitutions.

Genes encoding murine and human receptors for Nogo (NgR) have beendiscovered. Various domains in the NgR polypeptide have been identified,and certain of their functions have been discovered. In addition,important aspects of the interaction of specific regions of the Nogopolypeptide (ligand) with NgR have been discovered. Based on these andother discoveries, the invention features molecules and methods usefulfor decreasing Nogo-dependent inhibition of axonal growth in CNSneurons.

The invention includes a NgR-derived polypeptide that contains aminoacid residues 27-309 of SEQ ID NO:2 (human NgR NTLRRCT domain), whilecontaining fewer than 115 consecutive amino acids from amino acids310-445 of SEQ ID NO:2 (human NgR CTS domain). The NgR NTLRRCT domainoptionally includes up to 20 conservative amino acid substitutions. Insome embodiments, the encoded polypeptide contains fewer than 50consecutive amino acids from amino acids from the NgR CTS domain. Whilethe polypeptide may include a functional GPI domain, a functional GPIdomain may be absent, e.g., when a soluble polypeptide is desired. Theinvention also includes a nucleic acid encoding a NgR-derivedpolypeptide; a vector, e.g., operably linked to an expression controlsequence, containing the nucleic acid; and a transformed host cellcontaining the vector. The invention also includes a method of producinga NgR-derived polypeptide. The method includes introducing a nucleicacid encoding the above-described polypeptide into a host cell,culturing the host cell under conditions suitable for expression of saidpolypeptide, and recovering the polypeptide.

The invention also includes an antibody that binds to an epitope in theCTS domain of NgR. The antibody can be polyclonal or monoclonal.

The invention also includes a method of inhibiting binding of a Nogopolypeptide to a NgR. The method includes contacting the Nogopolypeptide with an effective amount of the above-described NgR-derivedpolypeptide.

The invention also includes a method of inhibiting binding of a Nogopolypeptide to a NgR, comprising contacting the NgR with an antibodythat binds to the amino acid sequence consisting of SEQ ID NO:2 (NgRpolypeptide).

The invention also includes a method of decreasing inhibition of axonalgrowth by a CNS neuron. The method includes contacting the neuron withan effective amount of: (a) an above-described NgR-derived polypeptide;or (b) an antibody that binds to the amino acid sequence set forth asSEQ ID NO:2 (NgR). In some embodiments of the invention, the antibodybinds to an epitope within the amino acid sequence consisting of aminoacids 310-445 of SEQ ID NO:2 (CTS domain of NgR).

The invention also includes a method of treating a central nervoussystem disease, disorder or injury, e.g., spinal cord injury. The methodincludes administering to a mammal, e.g., a human, an effective amountof: (a) an agent that inhibits binding of a Nogo polypeptide to a NgR;or (b) an agent that inhibits NgR-dependent signal transduction in acentral nervous system neuron. Exemplary agents for inhibiting bindingof a Nogo polypeptide to a NgR include: (a) an above-describedNgR-derived polypeptide; and (b) an antibody that binds to the NgRpolypeptide (SEQ ID NO:2). In some embodiments, the antibody binds to anepitope within the CTS domain of NgR (amino acids 310-445 of SEQ IDNO:2).

The invention also includes a method for identifying a molecule thatinhibits binding of a Nogo polypeptide to a NgR. The method includes:(a) providing a NgR polypeptide; (b) contacting the NgR polypeptide witha candidate molecule; and (c) detecting a decrease in binding of theNogo polypeptide to the NgR in the presence of the candidate molecule,as compared to the binding of the Nogo polypeptide to the NgR in thepresence of the candidate molecule.

The method also includes pharmaceutical compositions. In someembodiments the composition contains an above-described NgR-derivedpolypeptide and a pharmaceutically acceptable carrier. In otherembodiments, the composition contains an antibody that binds to anepitope in the NgR CTS domain, and a pharmaceutically acceptablecarrier.

The invention also includes a polypeptide that contains the amino acidsequence IYKGVIQAI or EELV, or both, with the polypeptide containing atotal of 40 amino acids or fewer (“Nogo ligand-derived polypeptide”). Insome embodiments, the Nogo ligand-derived polypeptide includes aminoacid residues 2 to 34 of SEQ ID NO:21. In some embodiments, the Nogoligand-derived polypeptide includes a heterologous amino acid sequencenot present in NogoA, wherein the heterologous amino acid sequencecontains at least five amino acid residues. The invention also includesa nucleic acid encoding a Nogo ligand-derived polypeptide; a vector,e.g., operably linked to an expression control sequence, containing thenucleic acid; and a transformed host cell containing the vector.

The invention also includes an antibody that binds to an above-describedNogo ligand-derived polypeptide. The antibody can be polyclonal ormonoclonal.

The invention also includes a composition that contains anabove-described NgR-derived polypeptide and a pharmaceuticallyacceptable carrier or an antibody that binds to an epitope in the NgRCTS domain, and a pharmaceutically acceptable carrier.

The invention also includes an alternative method of inhibiting bindingof a Nogo polypeptide to a NgR. The alternative method includescontacting the Nogo polypeptide with an effective amount of anabove-described Nogo ligand-derived polypeptide.

The invention also includes an alternative method of decreasinginhibition of axonal growth by a CNS neuron. The alternative methodincludes contacting the neuron with an effective amount of anabove-described Nogo ligand-derived polypeptide.

The invention also includes an alternative method of treating a centralnervous system disease, disorder or injury, e.g., a spinal cord injury.The alternative method includes administering to a mammal, e.g., ahuman, an effective amount of an above-described Nogo ligand-derivedpolypeptide.

The invention also includes a method of identifying a molecule thatdecreases Nogo-dependent inhibition of axonal growth. The methodincludes: (a) providing a polypeptide containing a target sequenceconsisting of IYKGVIQAI or EELV, or both; (b) contacting the polypeptidewith a candidate molecule; and (c) detecting binding of the candidatemolecule to a target sequence in the polypeptide.

The invention also includes embodiments wherein SEQ ID NO:4 (murine NgR)is substituted for SEQ ID NO:2 (human NgR). Those of skill in the artwill recognize where the human sequence is preferable over the murinesequence and visa versa.

DESCRIPTION OF THE FIGURES

FIGS. 1A-1I—Comparison of Nogo domains

FIG. 1A is a schematic diagram which summarizes features of the Nogoproteins utilized in this study.

FIG. 1B is a photograph of NIH-3T3 fibroblasts cultured on surfacescoated with Amino-Nogo, GST-Nogo-66 or no protein and stained forfilamentous actin (scale bar, 40 μm).

FIG. 1C is a photograph of chick E12 dorsal root ganglions cultured onsurfaces coated with Amino-Nogo, GST-Nogo-66 or no protein(substrate-bound) or with 100 nM Nogo protein (soluble) (scale bar, 40μm).

FIG. 1D is a photograph of a gel and an immunoblot where purifiedAmino-Nogo-Myc-His protein was subjected to SDS-PAGE and stained withCommassie Brilliant Blue (CBB) or immunoblotted with anti-Myc antibodies(Myc) (molecular weight markers of 200, 116, 97, 65 & 45 kDa are atleft).

FIG. 1E is a graph displaying experimental data where the percentage of3T3 fibroblasts with an area greater than 1200 μm² (spread) was measuredfrom experiments as in FIG. 1B on Nogo-coated surfaces (black) or withsoluble 100 nM Nogo preparations (blue) (AM, Amino-Nogo; AM+Myc,Amino-Nogo preincubated with anti-Myc antibody; AM+Myc+Mo, AM+Mycpreincubated with anti-mouse IgG antibody; Myc+Mo, anti-Myc antibodyplus anti-murine IgG antibody).

FIG. 1F is a graph displaying experimental data where the percentage ofspread COS-7 cells was determined after culture on Nogo-coated surfacesor with soluble 100 nM Nogo preparations.

FIG. 1G is a graph displaying experimental data where the effects ofpurified preparations of GST-Nogo-66 or Amino-Nogo on growth conemorphology was assessed in E12 dorsal root ganglion cultures at theindicated concentrations after thirty minutes. This demonstrates thatGST-Nogo-66 is two orders of magnitude more potent than Amino-Nogo inthis assay.

FIG. 1H is a graph displaying experimental data where the neuriteoutgrowth per cell in E13 dorsal root ganglion cultures was quantitatedfrom experiments as in (c) on Nogo-coated surfaces or with soluble 100nM Nogo preparations.

FIG. 1I is a graph displaying experimental data where the effects ofNogo preparations on neurite outgrowth in cerebellar granule neurons wasmeasured.

FIGS. 2A-2B—Nogo fragments antagonize Nogo and CNS myelin action

FIG. 2A is a photograph of chick E12 dorsal root ganglion explants thatwere cultured and growth cone collapse assessed as described in FIGS. 4Aand 4B. Cultures were exposed to the following preparations for thirtyminutes before fixation and staining with rhodamine-phalloidin: bufferonly (Control); 15 nM GST-Nogo); 1 μM each of Pep1, Pep2 and Pep3 (Pep);15 nM GST-Nogo plus 1 μM each of Pep1, Pep2 and Pep3 (Nogo+Pep). Notethat growth cone collapse by Nogo is blocked by peptide addition. Pep1,residues 1-25 of the extracellular domain; Pep2, 11-35; and Pep3, 21-45.

FIG. 2B is a graph quantifying the results from growth cone collapseassays as in FIG. 2A. Individual peptides were included at 4 μM, and thepeptide 1-3 mixture was 1 μM of each peptide. CNS myelin was prepared asdescribed and the indicated total myelin protein concentrations wereincluded in the cultures. All results are the means±s.e.m. calculatedfrom four to seven determinations. Those values significantly differentfrom the corresponding values with the same concentration of Nogo ormyelin but without peptide are indicated (asterisk, p<0.05, Student'stwo-tailed t test).

FIGS. 3A-3B—Nogo antagonist Pep2-41

FIG. 3A is a graph displaying the results of chick E12 dorsal rootganglion growth cone collapse assays. These assays were performed andquantified as in GrandPré et al., (2000) Nature 403, 439-444. Assayswere conducted with no addition (Control), 15 nM GST-Nogo or 15 nMGST-Nogo plus 1 μM Pep2-41 (Nogo+Pep). The values are means±s.e.m.calculated from four determinations.

FIG. 3B is a graph displaying the results of binding experiments wherebinding of 10 nM AP-Nogo to chick E12 dorsal root ganglion neurons wasmeasured as described in FIG. 4 with the addition of the indicatedconcentrations of Pep2-41.

FIGS. 4A-4B—Nogo Pep2-41 prevents both Nogo & CNS myelin inhibition ofneurite outgrowth

FIG. 4A is a graph which displays the results of outgrowth assays whereneurons were cultured in the presence of the indicated concentrations ofPep2-41 and purified GST-Nogo (GST-Nogo-66) protein. Chick E13 dorsalroot ganglion neurons were cultured under standard conditions. Foroutgrowth assays, neurons were cultured in the presence of the indicatedconcentrations of Pep2-41 and purified GST-Nogo (GST-Nogo-66) protein.This demonstrates that Pep2-41 can reverse the inhibition of neuriteoutgrowth by GST-Nogo.

FIG. 4B is a graph which displays the results of outgrowth assays whereneurons were cultured in the presence of the indicated concentrations ofPep2-41 and crude CNS myelin protein. This demonstrates that Pep2-41 canreverse the inhibition of neurite outgrowth by total CNS myelin.

FIGS. 5A-5F—Ligand binding assay for axonal Nogo receptors

FIG. 5A is a photograph of a gel and an immunoblot where the His-AP-Nogo(66 amino acid) protein was expressed in HEK293T cells, and purifiedfrom conditioned medium on a Nickel-containing resin via the His tag.Purified protein was subjected to SDS-PAGE and stained for total proteinwith CBB or immunoblotted with anti-Nogo antibodies (anti-Nogo).Molecular weight markers of 200, 116, 97, 65 and 45 kDa are shown atleft, and the migration of AP-Nogo at right. FIG. 5B is a photograph ofdissociated chick E12 dorsal root ganglion neurons that were incubatedwith 10 nM AP-Nogo or 10 nM AP-Nogo+160 nM GST-Nogo for sixty minutes at23° C. The cells were washed, fixed and incubated at 60° C. in order toinactivate endogenous AP. Bound AP-Nogo was detected by incubation withnitro blue tetrazolium. Note the intense neuronal staining by AP-Nogothat is displaced by unlabeled ligand.

FIG. 5C is a graph displaying experimental data where the potency ofAP-Nogo and GST-Nogo in E12 chick dorsal root ganglion growth conecollapse assays was assessed as described in the Example section. TheEC50 of AP-Nogo was determined to be 1 nM or less. The means±s.e.m.calculated from five to eight determinations are illustrated.

FIG. 5D is a graph displaying experimental data where the binding of 10nM AP-Nogo to chick E12 dorsal root ganglion neurons was assessed alone,or in the presence of 100 nM GST-Nogo or in the presence of 4 μM Pep2,which was quantified from experiments as in FIG. 5B by the methoddescribed in the Example section. The means±s.e.m. calculated from eightdeterminations are shown.

FIG. 5E is a graph displaying experimental data where AP-Nogo binding todorsal root ganglion neurons was measured as a function of AP-Nogoconcentration. This is one of six experiments with similar results.

FIG. 5F is a graph summarizing the data from FIG. 5E replotted forScatchard analysis. The apparent Kd for AP-Nogo binding to E12 chickdorsal root ganglion neurons is 3 nM.

FIG. 6—Nogo binding to COS-7 expressing the Nogo receptor

This figure is a photograph of COS-7 cells that were transfected with anexpression vector encoding the murine NgR. Two days after transfection,binding of AP-Nogo or AP was assessed as described in the Examplesection for dorsal root ganglion neurons. Note the selective binding ofAP-Nogo to NgR expressing cells. Binding is greatly reduced in thepresence of excess Nogo peptide not fused to AP.

FIG. 7—Structure of the Nogo receptor

This schematic diagram illustrates the major structural features of theNgR.

FIG. 8—Distribution of NgR mRNA.

This figure is a photograph of Northern blot of NgR mRNA for polyA+ RNAsamples from the indicated murine tissues on the left and for total RNAsamples from various rat brain regions on the right. The migration ofRNA size markers is shown at left.

FIGS. 9A-9C—Nogo-66 Receptor Immunohistology

FIG. 9A is a photograph of an immunoblot where membrane fractions (10 μgprotein) from the indicated cells or chick tissues were analyzed byanti-Nogo-66 receptor immunoblot (molecular weight markers in kDa are atright).

FIG. 9B is a photograph of COS-7 cells expressing Myc-Nogo-66 receptoror chick E5 spinal cord explants (eight days in vitro) stained withanti-Nogo-66 receptor, anti-Myc or the oligodendrocyte-specific O4antibody. The bottom three panels show double label immunohistochemistryof the same field (scale bar, 40 μm for the top three panels and 80 μmfor the bottom three panels).

FIG. 9C is a photograph of paraformaldehyde-fixed vibratome sections ofadult brain or spinal cord stained with the anti-Nogo-66 receptorpreparation. This demonstrates staining of axonal profiles (arrows) inboth the pons and spinal cord. Staining is dramatically reduced in thepresence of 10 μg/ml GST-Nogo-66 receptor antigen.

FIGS. 10A-10E—Nogo-66 Receptor mediates growth cone collapse by Nogo-66

FIG. 10A is a photograph of chick E12 DRG explants exposed to Nogo-66following pre-treatment with PI-PLC or buffer. Staining of F-actin inaxons is illustrated (scale bar, 40 μm).

FIG. 10B is a graph summarizing the experimental results of binding of 3nM AP or AP-Nogo to chick E12 dorsal root ganglion dissociated neurons.Where indicated the cultures were pre-treated with PI-PLC or 150 nMGST-Nogo-66 was included in the incubation with AP-Nogo.

FIG. 10C is a graph summarizing growth cone collapse measurements fromexperiments as in FIG. 10A. Chick E12 DRG cultures were treated with orwithout PI-PLC prior to exposure to 30 nM GST-Nogo-66 or 100 pM Sema3A.

FIG. 10D is a photograph of E7 retinal ganglion cell explants infectedwith a control virus (HSV-PlexinA1) or with HSV-Myc-Nogo-66 receptor andthen incubated with or without Nogo-66. Phalloidin staining of axonalgrowth cones is illustrated (scale bar, 25 μm).

FIG. 10E is a graph quantitating growth cone collapse in uninfected, orviral infected E7 retinal neurons as in FIG. 10D.

FIGS. 11A-11B—Structure-function analysis of Nogo-66 receptor

FIG. 11A is a schematic diagram of different Nogo-66 receptor deletionmutants. These mutants were assessed for level of expression byimmunoblot and for AP-Nogo binding. Note that the leucine rich repeatsand the leucine rich repeat carboxy terminal are required for Nogobinding but the remainder of the protein is not. The second protein wastested after purification and immobilization.

FIG. 11B is a diagram of the predicted three dimensional structure forthe first seven leucine rich repeats of the Nogo-66 receptor. This isderived from computer modeling based on the predicted structure of therelated leucine rich repeats of the leutropin receptor (Jiang et al.,(1995) Structure 3, 1341-1353). Modeling is performed by Swiss-Model atThe Expert Protein Analysis System (ExPASy) proteomics server of theSwiss Institute of Bioinformatics (SIB) (expasy.ch/spdbv). Those regionswith beta sheet and alpha helix secondary structure are also indicated.

FIGS. 12A-12B—Soluble NgR blocks Nogo-66

FIG. 12A shows photographs demonstrating that central nervous systemmyelin inhibits outgrowth and that this is blocked by the presence theNgR ectodomain protein. Chick E13 DRG neurons were cultured understandard conditions.

FIG. 12B demonstrates that Nogo-induced collapse is blocked by thesoluble receptor fragment. In growth cone collapse assays, conditionedmedium from HEK 293T cells secreting the 1-348 amino acid ectodomainfragment of the murine NgR or control conditioned medium was addedtogether with 100 nM Nogo-66.

FIG. 12C shows the quantification of the outgrowth assay. For outgrowthassays, neurons were cultured in the presence of control or NgRectodomain conditioned medium together with Nogo-66 protein (50 nM) orcentral nervous system myelin (15 μg total protein/ml).

FIGS. 13A-13B—Regions in the luminal/extracellular domain of Nogonecessary for NgR binding

FIG. 13A graphically depicts the amino acid sequences of peptidesderived from the luminal/extracelluar domain of Nogo that wererecombinantly attached to DNA encoding alkaline phosphatase (AP) andexpressed to make AP fusion proteins. FIG. 13B shows the binding of theabove AP fusion proteins to COS-7 cells expressing NgR. Conditionedmedium from 293T cells expressing the AP fusion proteins or AP alone wasapplied to COS-7 cells transfected with mouse NgR (mNgR). Binding wasvisualized after application of substrates NBT and BCIP. Scale bar, 100um.

FIGS. 14A-14C—Residues 1-40 of the luminal/extracellular domain of Nogobind NgR

FIG. 14A shows the binding of the fusion protein containing AP and the1-40 peptide described in FIG. 5A [hereinafter “140-AP”] to COS-7 cellsexpressing mouse NgR. Scale bar, 100 um. FIG. 14B graphically depictsthe binding of 140-AP to COS-7 cells expressing mNgR as measured as afunction of 140-AP concentration. FIG. 14C graphically depicts dataderived from the above 140-AP binding assay replotted as bound/free v.bound. The Kd of 140-AP binding to mNgR in this assay is 8 nM.

FIGS. 15A-15B—Growth cone collapsing activity AP-fused peptides

FIG. 15A shows E12 chick DRG growth cone morphology following 30 minuteexposure to 140-AP and AP-Nogo-66 fusion proteins. Scale bar, 25 um.FIG. 15B graphically depicts the quantification of growth cone collapsein E12 chick DRG cultures after exposure to condition medium containing20 nM AP fusion proteins comprising AP fused to the following peptidesas described in FIG. 13A: 1-66, 1-40, 1-35 and 6-40. As a control,condition medium containing no AP fusion protein was used.

FIGS. 16A-16E—Peptide 140 neutralizes Nogo-66 inhibitory activity

FIG. 16A shows E12 chick DRG growth cone morphology after treatment witha synthetic peptide encoding amino acids #1055-1094, acetylated at theC-terminus and amidated at the N-terminus of the human NogoA protein[hereinafter, “peptide 140”], the luminal/extracellular space encoded bySEQ ID NO:22. The cultures were pretreated with 1 uM peptide 140 orbuffer followed by a 30 minute exposure to 30 nM GST-Nogo-66 or 12.5 nMTPA. The amino acid sequence of peptide 140 corresponds to a sequencewithin the luminal/extracellular region of the hNogo protein. Scale bar25 um. Growth cones were visualized by rhodamine-phalloidin staining.FIG. 16B, FIG. 16C, and FIG. 16D graphically depict the amount of E12chick DRG growth cone collapse after the cells have been pretreated with1 uM peptide 140, or buffer before a 30 minute exposure to variousconcentrations of GST-Nogo-66, TPA or Sema3A. FIG. 16E graphicallydepicts, as compared to a control, the percentage of neurite outgrowthin dissociated E12 chick DRG cultures grown for 5-7 hours in thepresence of substrate coated with GST-Nogo-66 or phosphate bufferedsaline (PBS) following treatment with peptide 140, a scrambled versionof peptide 140 (i.e.,acetyl-SYVKEYAPIFAGKSRGEIKYQSIEIHEAQVRSDELVQSLN-amide) or buffer.

FIGS. 17A-17C—Peptide 140 partially blocks CNS myelin inhibitoryactivity

FIG. 17A shows dissociated E12 chick DRG cultures grown on boundsubstrate coating (CNS myelin or PBS) following treatment with 1 uMpeptide 140, a scrambled version of peptide 140 or buffer. Scale bar 75um. FIG. 17B graphically depicts the percentage of E12 chick DRG growthcone collapse in explant cultures pretreated with peptide 140 or bufferand then exposed to CNS myelin or PBS for 30 minutes before fixation.FIG. 17C graphically depicts the percentage of neurite outgrowth for E12chick dissociated DRG neurite outgrowth grown for 5-7 hours on boundsubstrate coating (CNS myelin or PBS) following application of peptide140, scrambled peptide 140 or buffer.

FIGS. 18A-18B. Nogo binding to NgR Deletion Mutants: LRRNT, LRR1-8 andLRRCT required for binding

FIG. 18A shows WTNgR (wt) and the NgR deletion mutants used in thisstudy. NgR mutants include deletions to the amino terminus (ANT), LRRdomains 1 and 2 (Δ1-2), LRR domains 3 and 4 (Δ3-4), LRR domains 5 and 6(Δ5-6), LRR domains 7 and 8 (Δ7-8), the LRR carboxy terminus (ΔLRRCT),the NgR carboxy terminus (ΔCT) and the complete LRR domain (LRR-). FIG.18B shows COS-7 cells transfected with NgR deletion mutant plasmids, andwere stained for anti-myc immunoreactivity or tested for AP-Nogobinding. All NgR mutant proteins were expressed in COS-7 cells as shownby myc immunoreactivity. Only wtNgR and NgRΔCT-transfected COS-7 cellsbound to AP-Nogo. Scale bar, 100 μm.

FIGS. 19A-19B. Expression of HSVNgR proteins in retinal ganglion cellneurites

FIG. 19A shows HSV plasmids encoding myc epitope-tagged wild-type NgR(mycNgR), L1NgR, and myc-tagged NgRΔCT were transfected into HEK293Tcells and protein expression in cell lysates was analyzed by SDS-PAGEand immunoblotting with anti-myc and anti-NgR antibodies. All threeproteins were expressed at the predicted molecular weight asdemonstrated by anti-NgR immunoblotting. L1NgR encodes residues 1-451 ofmouse NgR fused to the transmembrane and cytoplasmic tail of mouse L1,but lacks a myc tag. FIG. 19B:-Anti-myc immunostaining of infectedretinal explants demonstrates expression of mycNgRΔCT in RGC neuritesdouble stained with phalloidin. Myc-staining was negative in aphalloidin-stained neurite that was infected with HSVL1NgR.

FIGS. 20A-20B. NgRL1 mediates growth cone collapse in response toGST-hNogo-A(1055-1120) but NgRΔCT does not

FIG. 20A: E7 chick retinal explants were infected with recombinant viralpreparations of PlexinA1 (PlexA1), wild-type NgR (wtNgR), NgRL1 chimericreceptor (NgRL1), or NgR carboxy terminal deletion mutant (NgRΔCT).Explants were treated with GST-hNogo-A(1055-1120) for 30 min, andstained with rhodamine-phalloidin. Cells infected with PlexA1 virus orNgRΔCT virus are insensitive to treatment with GST-hNogo-A(1055-1120),whereas wtNgR or NgRL1-infected cells collapse in response toGST-hNogo-A(1055-1120). FIG. 20B: Dose curve of RGC response to varyingamounts of GST-hNogo-A(1055-1120) following infection with NgR viralpreparations.

FIG. 21. GSTNgRCT does not constitutively inhibit neurite outgrowth

Neurite outgrowth of dissociated E13 DRGs plated onGST-hNogo-A(1055-1120) substrates in the presence of 100 nM GSTNgRCT orPBS as a control. GSTNgRCT does not inhibit neurite outgrowth on controlPBS spots or modify the response of E13 DRGs to GST-hNogo-A(1055-1120)inhibition.

FIGS. 22A-22B. Analysis of NgR subcellular localization.

Cell lysates from HEK293T cells transfected with HSVwtNgR or HSVNgRL1plasmids were fractionated on OptiPrep flotation gradients. Fractionswere separated by SDS-PAGE and analyzed by immunoblotting blots withanti-NgR, anti-TfR, or anti-caveolin antibodies. As predicted, wtNgR isfound almost exclusively in the caveolin-rich detergent insolublefraction as shown in FIG. 22A, whereas L1NgR is localized to multiplemembrane fractions with a much smaller proportion in the caveolin-richdetergent insoluble fraction compared to wtNgR as shown in FIG. 22B.

FIG. 23. mNgR binds to mNgR

COS-7 cells were transfected with wtNgR or NgR deletion mutant plasmidsand tested for AP-NgR binding. wtNgR and NgRΔCT-transfected COS-7 cellsbind to AP-NgR whereas other NgR deletion mutants do not. Scale bar, 100μm.

FIG. 24. The soluble ectodomain of mNgR blocks inhibition of outgrowthby soluble hNogo-A(1055-1120) and CNS myelin

Chick E13 DRG neurons were cultured under standard conditions. In growthcone collapse assays, conditioned medium from HEK293T cells secretingthe 1-348 as ectodomain fragment of the mNgR or control conditionedmedium was added together with 100 nM GST-hNogo-A(1055-1120). In thebottom left panel, note that hNogo-A(1055-1120)-induced collapse isblocked by the soluble receptor fragment. For outgrowth assays, neuronswere cultured in the presence of control or mNgR ectodomain conditionedmedium together with GST-hNogo-A(1055-1120) protein (50 nM) or CNSmyelin (15 μg total protein/ml). The top four panels show that CNSmyelin inhibits outgrowth and that this is blocked by the presence themNgR ectodomain protein.

DETAILED DESCRIPTION OF THE INVENTION I. Definitions

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Although any methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of the present invention, the preferred methodsand materials are described.

As used herein, the term “axon” refers to a long cellular protrusionfrom a neuron, whereby efferent (outgoing) action potentials areconducted from the cell body towards target cells.

As used herein, the term “axonal growth” refers to an extension of thelong process or axon, originating at the cell body and preceded by thegrowth cone.

As used herein, the term “central nervous system disease, disorder orinjury” refers to any state associated with abnormal function of thecentral nervous system (CNS). The term includes, but is not limited to,altered CNS function resulting from physical trauma to cerebral orspinal chord tissue, viral infection, autoimmune mechanism, geneticmutation and neurodegenerative diseases or disorders.

As used herein, the term “chimeric protein” refers to any polypeptidewhich is not completely homologous at the amino acid level to itswild-type sequence or is encoded by a nucleic acid which is derived fromsplicing two distinct sources of nucleic acids. The term includes, butis not limited to, fusion proteins and proteins designed to contain oneor more amino acid substitutions which distinguishes their amino acidsequence from the wild type sequence.

As used herein, the term “demyelinating disease” refers to apathological disorder characterized by the degradation of the myelinsheath of the oligodendrocyte cell membrane.

As used herein, the term “growth cone” refers to a specialized region atthe tip of a growing neurite that is responsible for sensing the localenvironment and moving the axon toward its appropriate synaptic targetcell.

As used herein, the term “growth cone movement” refers to the extensionor collapse of the growth cone toward a neuron's target cell.

As used herein, the term “neurite” refers to a process growing out of aneuron. As it is sometimes difficult to distinguish a dendrite from anaxon in culture, the term neurite is used for both.

As used herein, the term “oligodendrocyte” refers to a neuroglial cellof the CNS whose function is to myelinate CNS axons.

As used herein, the term “polypeptide” refers to a peptide which onhydrolysis yields more than two amino acids, called tripeptides,tetrapeptides, etc. according to the number of amino acids contained inthe polypeptide. The term “polypeptide” is used synonomously with theterm “protein” and “peptide” throughout the specification.

II. Specific Embodiments A. NgR Protein and Peptide Agents for the NgRProtein

The present invention provides isolated protein, allelic variants of theprotein, and conservative amino acid substitutions of the protein. Asused herein, the protein or polypeptide refers to a NgR protein that hasthe human amino acid sequence depicted in SEQ ID NO: 2 or the murineamino acid sequence depicted in SEQ ID NO: 4. The protein or polypeptidealso refers to the peptides identified as NgR peptide agents that havethe amino acid sequences depicted in SEQ ID NO: 8, 10, 12, 14, 16, 18and 20. The invention also includes naturally occurring allelic variantsand proteins that have a slightly different amino acid sequence thanthat specifically recited above. Allelic variants, though possessing aslightly different amino acid sequence than those recited above, willstill have the same or similar biological functions associated with thehuman and murine NgR proteins and the NgR peptide agents depicted in SEQID NO: 2, 4, 8, 10, 12, 14, 16, 18 and 20.

As used herein, the family of proteins related to the NgR proteinsrefers to proteins that have been isolated from organisms in addition tohumans and mice. The methods used to identify and isolate other membersof the family of proteins related to the NgR proteins are describedbelow.

The NgR proteins and peptide agents of the present invention arepreferably in isolated form. As used herein, a protein or ligand is saidto be isolated when physical, mechanical or chemical methods areemployed to remove the protein from cellular constituents that arenormally associated with the protein. A skilled artisan can readilyemploy standard purification methods to obtain an isolated protein orligand.

The proteins of the present invention further include conservativevariants of the proteins and ligands herein described. As used herein, aconservative variant refers to alterations in the amino acid sequencethat do not adversely affect the biological functions of the protein. Asubstitution, insertion or deletion is said to adversely affect theprotein when the altered sequence prevents or disrupts a biologicalfunction associated with the protein. For example, the overall charge,structure or hydrophobic-hydrophilic properties of the protein can bealtered without adversely affecting a biological activity. Accordingly,the amino acid sequence can be altered, for example to render thepeptide more hydrophobic or hydrophilic, without adversely affecting thebiological activities of the protein.

The allelic variants, the conservative substitution variants, and themembers of the protein family, will have an amino acid sequence havingat least seventy-five percent amino acid sequence identity with thehuman and murine sequences set forth in SEQ ID NO: 2, 4, 8, 10, 12, 14,16, 18 and 20, more preferably at least eighty percent, even morepreferably at least ninety percent, and most preferably at leastninety-five percent. Identity or homology with respect to such sequencesis defined herein as the percentage of amino acid residues in thecandidate sequence that are identical with the known peptides, afteraligning the sequences and introducing gaps, if necessary, to achievethe maximum percent homology, and not considering any conservativesubstitutions as part of the sequence identity. N-terminal, C-terminalor internal extensions, deletions, or insertions into the peptidesequence shall not be construed as affecting homology.

Thus, the proteins and peptides of the present invention includemolecules comprising the amino acid sequence of SEQ ID NO: 2, 4, 8, 10,12, 14, 16, 18 and 20; fragments thereof having a consecutive sequenceof at least about 3, 4, 5, 6, 10, 15, 20, 25, 30, 35 or more amino acidresidues of the NgR proteins and peptide agents; amino acid sequencevariants of such sequences wherein at least one amino acid residue hasbeen inserted N- or C-terminal to, or within, the disclosed sequence;amino acid sequence variants of the disclosed sequences, or theirfragments as defined above, that have been substituted by anotherresidue. Contemplated variants further include those containingpredetermined mutations by, e.g., homologous recombination,site-directed or PCR mutagenesis, and the corresponding proteins ofother animal species, including but not limited to rabbit, rat, porcine,bovine, ovine, equine and non-human primate species, the alleles orother naturally occurring variants of the family of proteins; andderivatives wherein the protein has been covalently modified bysubstitution, chemical, enzymatic, or other appropriate means with amoiety other than a naturally occurring amino acid (for example, adetectable moiety such as an enzyme or radioisotope).

As described below, members of the family of proteins can be used: (1)to identify agents which modulate at least one activity of the protein,(2) in methods of identifying binding partners for the protein, (3) asan antigen to raise polyclonal or monoclonal antibodies, and 4) as atherapeutic agent.

B. Nucleic Acid Molecules

The present invention further provides nucleic acid molecules thatencode the proteins and peptides comprising the amino acid sequence ofSEQ ID NO: 2, 4, 8, 10, 12, 14, 16, 18 and 20 and the related proteinsherein described, preferably in isolated form. As used herein, “nucleicacid” includes genomic DNA, cDNA, mRNA and antisense molecules, as wellas nucleic acids based on alternative backbones or including alternativebases whether derived from natural sources or synthesized.

Homology or identity is determined by BLAST (Basic Local AlignmentSearch Tool) analysis using the algorithm employed by the programsblastp, blastn, blastx, tblastn and tblastx (Karlin et al., (1990) Proc.Natl. Acad. Sci. USA 87, 2264-2268 and Altschul, (1993) J. Mol. Evol.36, 290-300, fully incorporated by reference) which are tailored forsequence similarity searching. The approach used by the BLAST program isto first consider similar segments between a query sequence and adatabase sequence, then to evaluate the statistical significance of allmatches that are identified and finally to summarize only those matcheswhich satisfy a preselected threshold of significance. For a discussionof basic issues in similarity searching of sequence databases seeAltschul et al., (1994) Nature Genetics 6, 119-129 which is fullyincorporated by reference. The search parameters for histogram,descriptions, alignments, expect (i.e., the statistical significancethreshold for reporting matches against database sequences), cutoff,matrix and filter are at the default settings. The default scoringmatrix used by blastp, blastx, tblastn, and tblastx is the BLOSUM62matrix (Henikoff et al., (1992) Proc. Natl. Acad. Sci. USA 89,10915-10919, fully incorporated by reference). Four blastn parameterswere adjusted as follows: Q=10 (gap creation penalty); R=10 (gapextension penalty); wink=1 (generates word hits at every wink^(th)position along the query); and gapw=16 (sets the window width withinwhich gapped alignments are generated). The equivalent Blastp parametersettings were Q=9; R=2; wink=1; and gapw=32. A Bestfit comparisonbetween sequences, available in the GCG package version 10.0, uses DNAparameters GAP=50 (gap creation penalty) and LEN=3 (gap extensionpenalty) and the equivalent settings in protein comparisons are GAP=8and LEN=2.

As used herein, “high stringency conditions” means hybridization at 42°C. in the presence of 50% formamide, followed by a first wash at 65° C.with 2×SSC containing 1% sodium SDS, followed by a second wash at 65° C.with 0.1×SSC.

As used herein, a nucleic acid molecule is said to be “isolated” whenthe nucleic acid molecule is substantially separated from contaminantnucleic acid encoding other polypeptides from the source of nucleicacid.

The present invention further provides fragments of the encoding nucleicacid molecule. As used herein, a fragment of an encoding nucleic acidmolecule refers to a portion of the entire protein encoding sequence.The size of the fragment will be determined by the intended use. Forexample, if the fragment is chosen so as to encode an active portion ofthe protein, the fragment will need to be large enough to encode thefunctional region(s) of the protein. If the fragment is to be used as anucleic acid probe or PCR primer, then the fragment length is chosen soas to obtain a relatively small number of false positives duringprobing/priming.

Fragments of the encoding nucleic acid molecules of the presentinvention (i.e., synthetic oligonucleotides) that are used as probes orspecific primers for the polymerase chain reaction (PCR) or tosynthesize gene sequences encoding proteins of the invention can easilybe synthesized by chemical techniques, for example, the phosphotriestermethod of Matteucci et al., (1981) J. Am. Chem. Soc. 103, 3185-3191 orusing automated synthesis methods. In addition, larger DNA segments canreadily be prepared by well known methods, such as synthesis of a groupof oligonucleotides that define various modular segments of the gene,followed by ligation of oligonucleotides to build the complete modifiedgene.

The encoding nucleic acid molecules of the present invention may furtherbe modified so as to contain a detectable label for diagnostic and probepurposes. A variety of such labels are known in the art and can readilybe employed with the encoding molecules herein described. Suitablelabels include, but are not limited to, biotin, radiolabeled nucleotidesand the like. A skilled artisan can employ any of the art known labelsto obtain a labeled encoding nucleic acid molecule.

Modifications to the primary structure by deletion, addition, oralteration of the amino acids incorporated into the protein sequenceduring translation can be made without destroying the activity of theprotein. Such substitutions or other alterations result in proteinshaving an amino acid sequence encoded by a nucleic acid falling withinthe contemplated scope of the present invention.

The NgR domain designations used herein are defined as follows:

TABLE 1 Example NgR domains Domain hNgR (SEQ ID: 2) mNgR (SEQ ID NO: 4)Signal Seq.  1-26  1-26 LRRNT 27-56 27-56 LRR1 57-81 57-81 LRR2  82-105 82-105 LRR3 106-130 106-130 LRR4 131-154 131-154 LRR5 155-178 155-178LRR6 179-202 179-202 LRR7 203-226 203-226 LRR8 227-250 227-250 LRRCT260-309 260-309 CTS (CT 310-445 310-445 Signaling) GPI 446-473 456-473

In some embodiments of the invention, the above domains are modified.

Modification can be in a manner that preserves domain functionality.Modification can include addition, deletion, or substitution of certainamino acids. Exemplary modifications include conservative amino acidsubstitutions. Preferably such substitutions number 20 or fewer per 100residues. More preferably, such substitutions number 10 or fewer per 100residues. Further exemplary modifications include addition of flankingsequences of up to five amino acids at the N terminus and/or C terminusof one or more domains.

According to this invention, the signal sequence and GPI domains of theNgRs of this invention can be replaced by signal sequences and GPIdomains of other proteins. In one embodiment of this invention, thesignal sequence domain consists of #1-26 of the hNgR or #1-26 of themNgR. The GPI domain function have been shown to anchor the proteins tolipid rafts (e.g., Tansey et al., Neuron 25:611-623 (2000)). GPI domainsare known in the art, e.g., Gaudiz, et al., J. Biol. Chem.273(40):26202-26209 (1998). According to one embodiment of theinvention, the GPI domain consists of #446-473 amino acid residues ofhNgR or #456-473 amino acid residues of mNgR. Biologically activevariants of the GPI domain include polypeptides comprising amino acidsequences that anchor proteins to lipid rafts.

The LRRNT domain is a leucine rich repeat domain that is typicallyflanking the N-terminal side of the LRR1-8 domain.

Leucine rich domains are also known in the art, e.g., Kobe, B. et al.,TIES 19(10):415-421 (1994). In one embodiment of this invention, theLRR1 domain, LRR2 domain, LRR3 domain, LRR4 domain, LRR5 domain, LRR6domain, the LRR7 domain and the LRR8 domain (collectively, also known asLRR1-8 herein) consists of the amino acid residues as recited inTable 1. The LR1-8 shares sequence identity with several other leucinerich proteins. According to one embodiment of this invention, a LRRdomain of NgR is replaced with a LRR domain of another protein.

The LRRCT domain is a leucine rich repeat domain that is typicallyflanking the C-terminal side of the LRR1-8 domain. According to oneembodiment of the invention, the LRRCT domain consists of #-260-309residues of hNgR or mNgR. According to one embodiment of the invention,the LRRCT domain consists of #-260-305 residues of hNgR or mNgR.

A polypeptide comprising a LRRNT domain, a LRR1-8 domain and a LRRCTdomain (collectively, also referred to as a NTLRRCT domain (SEQ IDNO:55) herein) of NgR is contemplated. Biologically active variants ofNTLRRCT include polypeptides comprising the NTLRRCT domain that can bindNogo and/or can bind to NgR. According,

A CTS domain is an amino acid sequence within a NgR between the LRRCTand the GPI domain. According to one embodiment, the CTS domain can bedescribed by the residues recited above. A CTS domain according to thisinvention is involved in signalling a neuron in response to a Nogoligand binding to the NgR. A “portion of a CTS domain” is 20 or moreconsecutive amino acids of a CTS domain. A portion of a CTS domain canalso be selected from the group consisting of 30 or more, 40 or more,and 50 or more consecutive amino acids of a CTS domain. According to oneembodiment of this invention, a NgR family member is manipulated so thatthe CTS region or a portion thereof is deleted, mutated or blocked withanother agent so that it is not functional. In one embodiment, the CTSdomain consists of #310-445 amino acid residue of hNgR or mNgR, or#306-442 of hNgR (SEQ ID NO:53). According to another embodiment, aminoacid sequences that have a sequence identity to #310-445 amino acidresidue of hNgR or mNgR, or #306-442 of hNgR in the range of 85% ormore, 90% or more, 95% or more, 99% or more sequence identity arecontemplated.

C. Isolation of Other Related Nucleic Acid Molecules

As described above, the identification of the human nucleic acidmolecule having SEQ ID NO: 1, 3, 7, 9, 11, 13, 15, 17 and 19 allows askilled artisan to isolate nucleic acid molecules that encode othermembers of the NgR protein family in addition to the sequences hereindescribed. Further, the presently disclosed nucleic acid molecules allowa skilled artisan to isolate nucleic acid molecules that encode othermembers of the family of NgR proteins and peptide agents.

Essentially, a skilled artisan can readily use the amino acid sequenceof SEQ ID NO: 2, 4, 8, 10, 12, 14, 16, 18 and 20 or an immunogenicfragment thereof to generate antibody probes to screen expressionlibraries prepared from appropriate cells. Typically, polyclonalantiserum from mammals such as rabbits immunized with the purifiedprotein (as described below) or monoclonal antibodies can be used toprobe a mammalian cDNA or genomic expression library, such as lambdagtl1 library, to obtain the appropriate coding sequence for othermembers of the protein family. The cloned cDNA sequence can be expressedas a fusion protein, expressed directly using its own control sequences,or expressed by constructions using control sequences appropriate to theparticular host used for expression of the enzyme.

Alternatively, a portion of a coding sequence herein described can besynthesized and used as a probe to retrieve DNA encoding a member of theprotein family from any mammalian organism. Oligomers containing e.g.,approximately 18-20 nucleotides (encoding about a six to seven aminoacid stretch) can be prepared and used to screen genomic DNA or cDNAlibraries to obtain hybridization under stringent conditions orconditions of sufficient stringency to eliminate an undue level of falsepositives.

Additionally, pairs of oligonucleotide primers can be prepared for usein a polymerase chain reaction (PCR) to selectively clone an encodingnucleic acid molecule. A PCR denature/anneal/extend cycle for using suchPCR primers is well known in the art and can readily be adapted for usein isolating other encoding nucleic acid molecules.

D. Recombinant DNA Molecules Containing a Nucleic Acid Molecule

The present invention further provides recombinant DNA molecules (rDNA)that contain a coding sequence. As used herein, a rDNA molecule is a DNAmolecule that has been subjected to molecular manipulation. Methods forgenerating rDNA molecules are well known in the art, for example, seeSambrook et al., (1989) Molecular Cloning—A Laboratory Manual, ColdSpring Harbor Laboratory Press. In the preferred rDNA molecules, acoding DNA sequence is operably linked to expression control sequencesand vector sequences.

The choice of vector and expression control sequences to which one ofthe protein family encoding sequences of the present invention isoperably linked depends directly, as is well known in the art, on thefunctional properties desired (e.g., protein expression, and the hostcell to be transformed). A vector of the present invention may be atleast capable of directing the replication or insertion into the hostchromosome, and preferably also expression, of the structural geneincluded in the rDNA molecule.

Expression control elements that are used for regulating the expressionof an operably linked protein encoding sequence are known in the art andinclude, but are not limited to, inducible promoters, constitutivepromoters, secretion signals, and other regulatory elements. Preferably,the inducible promoter is readily controlled, such as being responsiveto a nutrient in the host cell's medium.

In one embodiment, the vector containing a coding nucleic acid moleculewill include a prokaryotic replicon, i.e., a DNA sequence having theability to direct autonomous replication and maintenance of therecombinant DNA molecule extra-chromosomally in a prokaryotic host cell,such as a bacterial host cell, transformed therewith. Such replicons arewell known in the art. In addition, vectors that include a prokaryoticreplicon may also include a gene whose expression confers a detectablemarker such as a drug resistance. Typical of bacterial drug resistancegenes are those that confer resistance to ampicillin or tetracycline.

Vectors that include a prokaryotic replicon can further include aprokaryotic or bacteriophage promoter capable of directing theexpression (transcription and translation) of the coding gene sequencesin a bacterial host cell, such as E. coli. A promoter is an expressioncontrol element formed by a DNA sequence that permits binding of RNApolymerase and transcription to occur. Promoter sequences compatiblewith bacterial hosts are typically provided in plasmid vectorscontaining convenient restriction sites for insertion of a DNA segmentof the present invention. Examples of such vector plasmids are pUC8,pUC9, pBR322 and pBR329 (Biorad Laboratories), pPL and pKK223(Pharmacia). Any suitable prokaryotic host can be used to express arecombinant DNA molecule encoding a protein of the invention.

Expression vectors compatible with eukaryotic cells, preferably thosecompatible with vertebrate cells, can also be used to form a rDNAmolecules that contains a coding sequence. Eukaryotic cell expressionvectors are well known in the art and are available from severalcommercial sources. Typically, such vectors are provided containingconvenient restriction sites for insertion of the desired DNA segment.Examples of such vectors are pSVL and pKSV-10 (Pharmacia), pBPV-1, pML2d(International Biotechnologies), pTDT1 (ATCC 31255) and the likeeukaryotic expression vectors.

Eukaryotic cell expression vectors used to construct the rDNA moleculesof the present invention may further include a selectable marker that iseffective in an eukaryotic cell, preferably a drug resistance selectionmarker. A preferred drug resistance marker is the gene whose expressionresults in neomycin resistance, i.e., the neomycin phosphotransferase(neo) gene. (Southern et al., (1982) J. Mol. Anal. Genet. 1, 327-341).Alternatively, the selectable marker can be present on a separateplasmid, the two vectors introduced by co-transfection of the host cell,and transfectants selected by culturing in the appropriate drug for theselectable marker.

E. Host Cells Containing an Exogenously Supplied Coding Nucleic AcidMolecule

The present invention further provides host cells transformed with anucleic acid molecule that encodes a protein of the present invention.The host cell can be either prokaryotic or eukaryotic. Eukaryotic cellsuseful for expression of a protein of the invention are not limited, solong as the cell line is compatible with cell culture methods andcompatible with the propagation of the expression vector and expressionof the gene product. Preferred eukaryotic host cells include, but arenot limited to, yeast, insect and mammalian cells, preferably vertebratecells such as those from a mouse, rat, monkey or human cell line.Examples of useful eukaryotic host cells include Chinese hamster ovary(CHO) cells available from the ATCC as CCL61, NIH Swiss mouse embryocells NIH-3T3 available from the ATCC as CRL1658, baby hamster kidneycells (BHK), and the like eukaryotic tissue culture cell lines.

Transformation of appropriate cell hosts with a rDNA molecule of thepresent invention is accomplished by well known methods that typicallydepend on the type of vector used and host system employed. With regardto transformation of prokaryotic host cells, electroporation and salttreatment methods can be employed (see, for example, Sambrook et al.,(1989) Molecular Cloning—A Laboratory Manual, Cold Spring HarborLaboratory Press; Cohen et al., (1972) Proc. Natl. Acad. Sci. USA 69,2110-2114). With regard to transformation of vertebrate cells withvectors containing rDNA, electroporation, cationic lipid or salttreatment methods can be employed (see, for example, Graham et al.,(1973) Virology 52, 456-467; Wigler et al., (1979) Proc. Natl. Acad.Sci. USA 76, 1373-1376).

Successfully transformed cells, i.e., cells that contain a rDNA moleculeof the present invention, can be identified by well known techniquesincluding the selection for a selectable marker. For example, cellsresulting from the introduction of an rDNA of the present invention canbe cloned to produce single colonies. Cells from those colonies can beharvested, lysed and their DNA content examined for the presence of therDNA using a method such as that described by Southern, (1975) J. Mol.Biol. 98, 503-517 or the proteins produced from the cell assayed via animmunological method.

F. Production of Recombinant Proteins Using a rDNA Molecule

The present invention further provides methods for producing a proteinof the invention using nucleic acid molecules herein described. Ingeneral terms, the production of a recombinant form of a proteintypically involves the following steps:

First, a nucleic acid molecule is obtained that encodes a protein of theinvention, such as the nucleic acid molecule depicted in SEQ ID NO: 1,3, 7, 9, 11, 13, 15, 17 and 19 or nucleotides 166-1584 of SEQ ID NO: 1and nucleotides 178-1596 of SEQ ID NO: 3. If the encoding sequence isuninterrupted by introns, it is directly suitable for expression in anyhost.

The nucleic acid molecule is then preferably placed in operable linkagewith suitable control sequences, as described above, to form anexpression unit containing the protein open reading frame. Theexpression unit is used to transform a suitable host and the transformedhost is cultured under conditions that allow the production of therecombinant protein. Optionally the recombinant protein is isolated fromthe medium or from the cells; recovery and purification of the proteinmay not be necessary in some instances where some impurities may betolerated.

Each of the foregoing steps can be done in a variety of ways. Forexample, the desired coding sequences may be obtained from genomicfragments and used directly in appropriate hosts. The construction ofexpression vectors that are operable in a variety of hosts isaccomplished using appropriate replicons and control sequences, as setforth above. The control sequences, expression vectors, andtransformation methods are dependent on the type of host cell used toexpress the gene and were discussed in detail earlier. Suitablerestriction sites can, if not normally available, be added to the endsof the coding sequence so as to provide an excisable gene to insert intothese vectors. A skilled artisan can readily adapt any host/expressionsystem known in the art for use with the nucleic acid molecules of theinvention to produce recombinant protein.

G. Methods to Identify Binding Partners

The present invention provides methods for use in isolating andidentifying binding partners of proteins of the invention. In someembodiments, a protein of the invention is mixed with a potentialbinding partner or an extract or fraction of a cell under conditionsthat allow the association of potential binding partners with theprotein of the invention. After mixing, peptides, polypeptides, proteinsor other molecules that have become associated with a protein of theinvention are separated from the mixture. The binding partner bound tothe protein of the invention can then be removed and further analyzed.To identify and isolate a binding partner, the entire protein, forinstance the entire NgR protein of either SEQ ID NO: 2 or 4 or theentire Nogo protein of SEQ ID NO: 6 can be used. Alternatively, afragment of the protein can be used.

As used herein, a cellular extract refers to a preparation or fractionwhich is made from a lysed or disrupted cell. The preferred source ofcellular extracts will be cells derived from human brain or spinal cordtissue, for instance, human cerebral tissue. Alternatively, cellularextracts may be prepared from any source of neuronal tissue or availableneuronal cell lines, particularly olgiodendrocyte derived cell lines.

A variety of methods can be used to obtain an extract of a cell. Cellscan be disrupted using either physical or chemical disruption methods.Examples of physical disruption methods include, but are not limited to,sonication and mechanical shearing. Examples of chemical lysis methodsinclude, but are not limited to, detergent lysis and enzyme lysis. Askilled artisan can readily adapt methods for preparing cellularextracts in order to obtain extracts for use in the present methods.

Once an extract of a cell is prepared, the extract is mixed with theprotein of the invention under conditions in which association of theprotein with the binding partner can occur. A variety of conditions canbe used, the most preferred being conditions that closely resembleconditions found in the cytoplasm of a human cell. Features such asosmolarity, pH, temperature, and the concentration of cellular extractused, can be varied to optimize the association of the protein with thebinding partner.

After mixing under appropriate conditions, the bound complex isseparated from the mixture. A variety of techniques can be utilized toseparate the mixture. For example, antibodies specific to a protein ofthe invention can be used to immunoprecipitate the binding partnercomplex. Alternatively, standard chemical separation techniques such aschromatography and density-sediment centrifugation can be used.

After removal of non-associated cellular constituents found in theextract, the binding partner can be dissociated from the complex usingconventional methods. For example, dissociation can be accomplished byaltering the salt concentration or pH of the mixture.

To aid in separating associated binding partner pairs from the mixedextract, the protein of the invention can be immobilized on a solidsupport. For example, the protein can be attached to a nitrocellulosematrix or acrylic beads. Attachment of the protein to a solid supportaids in separating peptide-binding partner pairs from other constituentsfound in the extract. The identified binding partners can be either asingle protein or a complex made up of two or more proteins.Alternatively, binding partners may be identified using the AlkalinePhosphatase fusion assay according to the procedures of Flanagan &Vanderhaeghen, (1998) Annu. Rev. Neurosci. 21, 309-345 or Takahashi etal., (1999) Cell 99, 59-69; the Far-Western assay according to theprocedures of Takayama et al., (1997) Methods Mol. Biol. 69, 171-184 orSauder et al., J. Gen. Virol. (1996) 77, 991-996 or identified throughthe use of epitope tagged proteins or GST fusion proteins.

Alternatively, the nucleic acid molecules of the invention can be usedin a yeast two-hybrid system. The yeast two-hybrid system has been usedto identify other protein partner pairs and can readily be adapted toemploy the nucleic acid molecules herein described (see StratageneHybrizap® two-hybrid system).

H. Methods to Identify Agents that Modulate Expression

The present invention provides methods for identifying agents thatmodulate the expression of a nucleic acid encoding the Nogo receptorprotein. The present invention also provides methods for identifyingagents that modulate the expression of a nucleic acid encoding the Nogoprotein. Such assays may utilize any available means of monitoring forchanges in the expression level of the nucleic acids of the invention.As used herein, an agent is said to modulate the expression of a nucleicacid of the invention, for instance a nucleic acid encoding the proteinhaving the sequence of SEQ ID NO: 2, 4 or 6, if it is capable of up- ordown-regulating expression of the nucleic acid in a cell.

In one assay format, cell lines that contain reporter gene fusionsbetween the open reading frame defined by nucleotides 166-1584 of SEQ IDNO: 1, or nucleotides 178-1596 of SEQ ID NO: 3, or nucleotides 135-3713of SEQ ID NO: 5, and any assayable fusion partner may be prepared.Numerous assayable fusion partners are known and readily available,including the firefly luciferase gene and the gene encodingchloramphenicol acetyltransferase (Alam et al., (1990) Anal. Biochem.188, 245-254). Cell lines containing the reporter gene fusions are thenexposed to the agent to be tested under appropriate conditions and time.Differential expression of the reporter gene between samples exposed tothe agent and control samples identifies agents which modulate theexpression of a nucleic acid encoding the protein having the sequence ofSEQ ID NO: 2, 4 or 6.

Additional assay formats may be used to monitor the ability of the agentto modulate the expression of a nucleic acid encoding a Nogo receptorprotein of the invention such as the protein having the amino acidsequence of SEQ ID NO: 2 or 4 or a Nogo protein having the amino acidsequence of SEQ ID NO: 6. For instance, mRNA expression may be monitoreddirectly by hybridization to the nucleic acids of the invention. Celllines are exposed to the agent to be tested under appropriate conditionsand time and total RNA or mRNA is isolated by standard procedures suchthose disclosed in Sambrook et al., (1989) Molecular Cloning—ALaboratory Manual, Cold Spring Harbor Laboratory Press.

Probes to detect differences in RNA expression levels between cellsexposed to the agent and control cells may be prepared from the nucleicacids of the invention. It is preferable, but not necessary, to designprobes which hybridize only with target nucleic acids under conditionsof high stringency. Only highly complementary nucleic acid hybrids formunder conditions of high stringency. Accordingly, the stringency of theassay conditions determines the amount of complementarity which shouldexist between two nucleic acid strands in order to form a hybrid.Stringency should be chosen to maximize the difference in stabilitybetween the probe:target hybrid and potential probe:non-target hybrids.

Probes may be designed from the nucleic acids of the invention throughmethods known in the art. For instance, the G+C content of the probe andthe probe length can affect probe binding to its target sequence.Methods to optimize probe specificity are commonly available in Sambrooket al., (1989) Molecular Cloning—A Laboratory Manual, Cold Spring HarborLaboratory Press or Ausubel et al., (1995) Current Protocols inMolecular Biology, Greene Publishing.

Hybridization conditions are modified using known methods, such as thosedescribed by Sambrook et al., (1989) and Ausubel et al., (1995) asrequired for each probe. Hybridization of total cellular RNA or RNAenriched for polyA+ RNA can be accomplished in any available format. Forinstance, total cellular RNA or RNA enriched for polyA+ RNA can beaffixed to a solid support and the solid support exposed to at least oneprobe comprising at least one, or part of one of the sequences of theinvention under conditions in which the probe will specificallyhybridize. Alternatively, nucleic acid fragments comprising at leastone, or part of one of the sequences of the invention can be affixed toa solid support, such as a silicon based wafer or a porous glass wafer.The wafer can then be exposed to total cellular RNA or polyA+ RNA from asample under conditions in which the affixed sequences will specificallyhybridize. Such wafers and hybridization methods are widely available,for example, those disclosed by Beattie, (1995) WO9511755. By examiningfor the ability of a given probe to specifically hybridize to a RNAsample from an untreated cell population and from a cell populationexposed to the agent, agents which up or down regulate the expression ofa nucleic acid encoding the Nogo receptor protein having the sequence ofSEQ ID NO: 2 or 4 are identified.

Hybridization for qualitative and quantitative analysis of mRNA may alsobe carried out by using a RNase Protection Assay (i.e., RPA, see Ma etal., Methods (1996) 10, 273-238). Briefly, an expression vehiclecomprising cDNA encoding the gene product and a phage specific DNAdependent RNA polymerase promoter (e.g., T7, T3 or SP6 RNA polymerase)is linearized at the 3′ end of the cDNA molecule, downstream from thephage promoter, wherein such a linearized molecule is subsequently usedas a template for synthesis of a labeled antisense transcript of thecDNA by in vitro transcription. The labeled transcript is thenhybridized to a mixture of isolated RNA (i.e., total or fractionatedmRNA) by incubation at 45° C. overnight in a buffer comprising 80%formamide, 40 mM Pipes, pH 6.4, 0.4 M NaCl and 1 mM EDTA. The resultinghybrids are then digested in a buffer comprising 40 μg/ml ribonuclease Aand 2 μg/ml ribonuclease. After deactivation and extraction ofextraneous proteins, the samples are loaded onto urea-polyacrylamidegels for analysis.

In another assay format, agents which effect the expression of theinstant gene products, cells or cell lines would first be identifiedwhich express said gene products physiologically. Cells and cell linesso identified would be expected to comprise the necessary cellularmachinery such that the fidelity of modulation of the transcriptionalapparatus is maintained with regard to exogenous contact of agent withappropriate surface transduction mechanisms and the cytosolic cascades.Further, such cells or cell lines would be transduced or transfectedwith an expression vehicle (e.g., a plasmid or viral vector) constructcomprising an operable non-translated 5′-promoter containing end of thestructural gene encoding the instant gene products fused to one or moreantigenic fragments, which are peculiar to the instant gene products,wherein said fragments are under the transcriptional control of saidpromoter and are expressed as polypeptides whose molecular weight can bedistinguished from the naturally occurring polypeptides or may furthercomprise an immunologically distinct tag. Such a process is well knownin the art (see, Sambrook et al., (1989) Molecular Cloning—A LaboratoryManual, Cold Spring Harbor Laboratory Press).

Cells or cell lines transduced or transfected as outlined above wouldthen be contacted with agents under appropriate conditions; for example,the agent comprises a pharmaceutically acceptable excipient and iscontacted with cells in an aqueous physiological buffer such asphosphate buffered saline (PBS) at physiological pH, Eagles balancedsalt solution (BSS) at physiological pH, PBS or BSS comprising serum orconditioned media comprising PBS or BSS and serum incubated at 37° C.Said conditions may be modulated as deemed necessary by one of skill inthe art. Subsequent to contacting the cells with the agent, said cellswill be disrupted and the polypeptides of the disruptate arefractionated such that a polypeptide fraction is pooled and contactedwith an antibody to be further processed by immunological assay (e.g.,ELISA, immunoprecipitation or Western blot). The pool of proteinsisolated from the “agent contacted” sample will be compared with acontrol sample where only the excipient is contacted with the cells andan increase or decrease in the immunologically generated signal from the“agent contacted” sample compared to the control will be used todistinguish the effectiveness of the agent.

I. Methods to Identify Agents that Modulate Activity

The present invention provides methods for identifying agents thatmodulate at least one activity of a NgR protein. The invention alsoprovides methods for identifying agents that modulate at least oneactivity of a Nogo protein. Such methods or assays may utilize any meansof monitoring or detecting the desired activity.

In one format, the specific activity of a NgR protein or Nogo protein,normalized to a standard unit, between a cell population that has beenexposed to the agent to be tested compared to an un-exposed control cellpopulation may be assayed. Cell lines or populations are exposed to theagent to be tested under appropriate conditions and time. Cellularlysates may be prepared from the exposed cell line or population and acontrol, unexposed cell line or population. The cellular lysates arethen analyzed with the probe.

Antibody probes can be prepared by immunizing suitable mammalian hostsutilizing appropriate immunization protocols using the NgR protein, Nogoprotein, NgR peptide agents or immunogenic fragments of any of theforegoing. To enhance immunogenicity, these proteins or fragments can beconjugated to suitable carriers. Methods for preparing immunogenicconjugates with carriers such as BSA, KLH or other carrier proteins arewell known in the art. In some circumstances, direct conjugation using,for example, carbodiimide reagents may be effective; in other instanceslinking reagents such as those supplied by Pierce Chemical Co. may bedesirable to provide accessibility to the hapten. The hapten peptidescan be extended at either the amino or carboxy terminus with a cysteineresidue or interspersed with cysteine residues, for example, tofacilitate linking to a carrier. Administration of the immunogens isconducted generally by injection over a suitable time period and withuse of suitable adjuvants, as is generally understood in the art. Duringthe immunization schedule, titers of antibodies are taken to determineadequacy of antibody formation.

While the polyclonal antisera produced in this way may be satisfactoryfor some applications, for pharmaceutical compositions, use ofmonoclonal preparations is preferred. Immortalized cell lines whichsecrete the desired monoclonal antibodies may be prepared using standardmethods, see e.g., Kohler & Milstein, (1992) Biotechnology 24, 524-526or modifications which effect immortalization of lymphocytes or spleencells, as is generally known. The immortalized cell lines secreting thedesired antibodies can be screened by immunoassay in which the antigenis the peptide hapten, polypeptide or protein. When the appropriateimmortalized cell culture secreting the desired antibody is identified,the cells can be cultured either in vitro or by production in ascitesfluid.

The desired monoclonal antibodies may be recovered from the culturesupernatant or from the ascites supernatant. The intact anti-Nogo oranti-NgR antibodies or fragments thereof can be used as e.g.,antagonists of binding between Nogo (ligand) and a NgR. Use ofimmunologically reactive fragments, such as the Fab, Fab′ of F(ab′)2fragments is often preferable, especially in a therapeutic context, asthese fragments are generally less immunogenic than the wholeimmunoglobulin.

The antibodies or fragments may also be produced, using currenttechnology, by recombinant means. Antibody regions that bindspecifically to the desired regions of the protein can also be producedin the context of chimeras with multiple species origin, for instance,humanized antibodies.

The antibody can therefore be a humanized antibody or human a antibody,see. e.g., in U.S. Pat. No. 5,585,089 or Riechmann et al., (1988) Nature332, 323-327.

Agents that are assayed in the above method can be randomly selected orrationally selected or designed. As used herein, an agent is said to berandomly selected when the agent is chosen randomly without consideringthe specific sequences involved in the association of the a protein ofthe invention alone or with its associated substrates, binding partners,etc. An example of randomly selected agents is the use a chemicallibrary or a peptide combinatorial library, or a growth broth of anorganism.

As used herein, an agent is said to be rationally selected or designedwhen the agent is chosen on a non-random basis which takes into accountthe sequence of the target site or its conformation in connection withthe agent's action. Agents can be rationally selected or rationallydesigned by utilizing the peptide sequences that make up these sites.For example, a rationally selected peptide agent can be a peptide whoseamino acid sequence is identical to the binding domain (SEQ ID NO: 20)of Nogo which interacts with the NgR. Alternatively, it can be afragment of the binding domain, e.g., SEQ ID NO: 8, 10, 12, 14, 16 and18.

The agents of the present invention can be, as examples, peptides,antibodies, antibody fragments, small molecules, vitamin derivatives, aswell as carbohydrates. Peptide agents of the invention can be preparedusing standard solid phase (or solution phase) peptide synthesismethods, as is known in the art. In addition, the DNA encoding thesepeptides may be synthesized using commercially available oligonucleotidesynthesis instrumentation and produced recombinantly using standardrecombinant production systems. The production using solid phase peptidesynthesis is necessitated if non-gene-encoded amino acids are to beincluded.

Another class of agents of the present invention are antibodies orfragments thereof that bind to a Nogo protein or NgR protein. Antibodyagents can be obtained by immunization of suitable mammalian subjectswith peptides, containing as antigenic regions, those portions of theprotein intended to be targeted by the antibodies.

J. High Throughput Assays

The power of high throughput screening is utilized to the search for newcompounds which are capable of interacting with the NgR protein. Forgeneral information on high-throughput screening (e.g., Devlin, (1998)High Throughput Screening, Marcel Dekker; U.S. Pat. No. 5,763,263). Highthroughput assays utilize one or more different assay techniques.

Immunodiagnostics and Immunoassays.

These are a group of techniques used for the measurement of specificbiochemical substances, commonly at low concentrations in complexmixtures such as biological fluids, that depend upon the specificity andhigh affinity shown by suitably prepared and selected antibodies fortheir complementary antigens. A substance to be measures must, ofnecessity, be antigenic—either an immunogenic macromolecule or ahaptenic small molecule. To each sample a known, limited amount ofspecific antibody is added and the fraction of the antigen combiningwith it, often expressed as the bound:free ratio, is estimated, using asindicator a form of the antigen labeled with radioisotope(radioimmunoassay), fluorescent molecule (fluoroimmunoassay), stablefree radical (spin immunoassay), enzyme (enzyme immunoassay), or otherreadily distinguishable label.

Antibodies can be labeled in various ways, including: enzyme-linkedimmunosorbent assay (ELISA); radioimmuno-assay (MA); fluorescentimmunoassay (FIA); chemiluminescent immunoassay (CLIA); and labeling theantibody with colloidal gold particles (immuNogold).

Common assay formats include the sandwhich assay, competitive orcompetition assay, latex agglutination assay, homogeneous assay,microtitre plate format and the microparticle-based assay.

Enzyme-Linked Immunosorbent Assay (ELISA).

ELISA is an immunochemical technique that avoids the hazards ofradiochemicals and the expense of fluorescence detection systems.Instead, the assay uses enzymes as indicators. ELISA is a form ofquantitative immunoassay based on the use of antibodies (or antigens)that are linked to an insoluble carrier surface, which is then used to“capture” the relevant antigen (or antibody) in the test solution. Theantigen-antibody complex is then detected by measuring the activity ofan appropriate enzyme that had previously been covalently attached tothe antigen (or antibody).

For information on ELISA techniques, see, for example, Crowther, (1995)ELISA-Theory and Practice (Methods in Molecular Biology), Humana Press;Challacombe & Kemeny, (1998) ELISA and Other Solid PhaseImmunoassays—Theoretical and Practical Aspects, John Wiley; Kemeny,(1991) A Practical Guide to ELISA, Pergamon Press; Ishikawa, (1991)Ultrasensitive and Rapid Enzyme Immunoassay (Laboratory Techniques inBiochemistry and Molecular Biology) Elsevier.

Colorimetric Assays for Enzymes.

Colorimetry is any method of quantitative chemical analysis in which theconcentration or amount of a compound is determined by comparing thecolor produced by the reaction of a reagent with both standard and testamounts of the compound, e.g., using a colorimeter or aspectrophotometer.

Standard colorimetric assays of beta-galactosidase enzymatic activityare well known to those skilled in the art (see, for example, Norton etal., (1985) Mol. Cell. Biol. 5, 281-290). A colorimetric assay can beperformed on whole cell lysates usingO-nitrophenyl-beta-D-galactopyranoside (ONPG, Sigma) as the substrate ina standard colorimetric beta-galactosidase assay (Sambrook et al.,(1989) Molecular Cloning—A Laboratory Manual, Cold Spring HarborLaboratory Press. Automated colorimetric assays are also available forthe detection of beta-galactosidase activity (see e.g., U.S. Pat. No.5,733,720).

Immunofluorescence Assays.

Immunofluorescence or immunofluorescence microscopy is a technique inwhich an antigen or antibody is made fluorescent by conjugation to afluorescent dye and then allowed to react with the complementaryantibody or antigen in a tissue section or smear. The location of theantigen or antibody can then be determined by observing the fluorescenceby microscopy under ultraviolet light.

For general information on immunofluorescent techniques, see, forexample, Knapp et al., (1978) Immunofluorescence and Related StainingTechniques, Elsevier; Allan, (1999) Protein Localization by FluorescentMicroscopy—A Practical Approach (The Practical Approach Series) OxfordUniversity Press; Caul, (1993) Immunofluorescence Antigen DetectionTechniques in Diagnostic Microbiology, Cambridge University Press. Fordetailed explanations of immunofluorescent techniques applicable to thepresent invention, see U.S. Pat. No. 5,912,176; U.S. Pat. No. 5,869,264;U.S. Pat. No. 5,866,319; and U.S. Pat. No. 5,861,259.

K. Uses for Agents that Modulate Activity

As provided in the Examples, the Nogo and NgR proteins and nucleicacids, such as the proteins having the amino acid sequence of SEQ ID NO:2, 4 or 6, are expressed in myelin derived from axon and dendrites.Agents that modulate or up- or down-regulate the expression of the Nogoor NgR protein or agents such as agonists or antagonists of at least oneactivity of the Nogo or NgR protein may be used to modulate biologicaland pathologic processes associated with the protein's function andactivity. The invention is particularly useful in the treatment of humansubjects.

Pathological processes refer to a category of biological processes whichproduce a deleterious effect. For example, expression of a protein ofthe invention may be associated with inhibition of axonal regenerationfollowing cranial, cerebral or spinal trauma, stroke or a demyelinatingdisease. Such demyelinating diseases include, but are not limited to,multiple sclerosis, monophasic demyelination, encephalomyelitis,multifocal leukoencephalopathy, panencephalitis, Marchiafava-Bignamidisease, pontine myelinolysis, adrenoleukodystrophy,Pelizaeus-Merzbacher disease, Spongy degeneration, Alexander's disease,Canavan's disease, metachromatic leukodystrophy and Krabbe's disease. Asused herein, an agent is said to modulate a pathological process whenthe agent reduces the degree or severity of the process. For instance, ademyelinating disease may be prevented or disease progression modulatedby the administration of agents which reduce, promote or modulate insome way the expression or at least one activity of a protein of theinvention.

In one example, administration of the Nogo peptide agents depicted inSEQ ID NO: 8, 10, 12, 14, 16, 18 and 20 can be used to treat ademyelinating disease associated with Nogo or the NgR protein. Inanother example, cells which express the peptide agents of the inventionmay be transplanted to a site spinal cord injury to facilitate axonalgrowth throughout the injured site. Such transplanted cells wouldprovide a means for restoring spinal cord function following injury ortrauma.

In yet another example, administration of soluble NgR protein that bindsto Nogo can be used to treat a demyelinating disease associated withNogo or the NgR protein. This agent can be used to prevent the bindingof Nogo to cell bound NgR and act as an antagonist of Nogo. Solublereceptors have been used to bind cytokines or other ligands to regulatetheir function (Thomson, (1998) Cytokine Handbook, Academic Press). Asoluble receptor occurs in solution, or outside of the membrane. Solublereceptors may occur because the segment of the molecule which spans orassociates with the membrane is absent. This segment is commonlyreferred to in the art as the transmembrane domain of the gene, ormembrane binding segment of the protein. Thus, in some embodiments ofthe invention, a soluble receptor includes a fragment or an analog of amembrane bound receptor. Preferably, the fragment contains at least six,e.g., ten, fifteen, twenty, twenty-five, thirty, forty, fifty, sixty, orseventy amino acids, provided it retains its desired activity.

In other embodiments of the invention, the structure of the segment thatassociates with the membrane is modified (e.g., DNA sequencepolymorphism or mutation in the gene) so the receptor is not tethered tothe membrane, or the receptor is inserted, but is not retained withinthe membrane. Thus, a soluble receptor, in contrast to the correspondingmembrane bound form, differs in one or more segments of the gene orreceptor protein that are important to its association with themembrane.

The agents of the present invention can be provided alone, or incombination, or in sequential combination with other agents thatmodulate a particular pathological process. For example, an agent of thepresent invention can be administered in combination withanti-inflammatory agents following stroke as a means for blockingfurther neuronal damage and inhibition of axonal regeneration. As usedherein, two agents are said to be administered in combination when thetwo agents are administered simultaneously or are administeredindependently in a fashion such that the agents will act at the sametime.

The agents of the present invention can be administered via parenteral,subcutaneous, intravenous, intramuscular, intraperitoneal, transdermal,or buccal routes. For example, an agent may be administered locally to asite of injury via microinfusion. Typical sites include, but are notlimited to, damaged areas of the spinal cord resulting from injury ordamaged sites in the brain resulting from a stroke. Alternatively, orconcurrently, administration may be by the oral route. The dosageadministered will be dependent upon the age, health, and weight of therecipient, kind of concurrent treatment, if any, frequency of treatment,and the nature of the effect desired.

The present invention further provides compositions containing one ormore agents which modulate expression or at least one activity of aprotein of the invention. While individual needs vary, determination ofoptimal ranges of effective amounts of each component is within theskill of the art. Typical dosages comprise 1 pg/kg to 100 mg/kg bodyweight. The preferred dosages for systemic administration comprise 100ng/kg to 100 mg/kg body weight. The preferred dosages for directadministration to a site via microinfusion comprise 1 ng/kg to 1 μg/kgbody weight.

In addition to the pharmacologically active agent, the compositions ofthe present invention may contain suitable pharmaceutically acceptablecarriers comprising excipients and auxiliaries which facilitateprocessing of the active compounds into preparations which can be usedpharmaceutically for delivery to the site of action. Suitableformulations for parenteral administration include aqueous solutions ofthe active compounds in water-soluble form, for example, water-solublesalts. In addition, suspensions of the active compounds as appropriateoily injection suspensions may be administered. Suitable lipophilicsolvents or vehicles include fatty oils, for example, sesame oil, orsynthetic fatty acid esters, for example, ethyl oleate or triglycerides.Aqueous injection suspensions may contain substances which increase theviscosity of the suspension include, for example, sodium carboxymethylcellulose, sorbitol and dextran. Optionally, the suspension may alsocontain stabilizers. Liposomes can also be used to encapsulate the agentfor delivery into the cell.

The pharmaceutical formulation for systemic administration according tothe invention may be formulated for enteral, parenteral or topicaladministration. Indeed, all three types of formulations may be usedsimultaneously to achieve systemic administration of the activeingredient. Suitable formulations for oral administration include hardor soft gelatin capsules, pills, tablets, including coated tablets,elixirs, suspensions, syrups or inhalations and controlled release formsthereof.

In practicing the methods of this invention, the agents of thisinvention may be used alone or in combination, or in combination withother therapeutic or diagnostic agents. In certain preferredembodiments, the compounds of this invention may be co-administeredalong with other compounds typically prescribed for these conditionsaccording to generally accepted medical practice, such asanti-inflammatory agents, anticoagulants, antithrombotics, includingplatelet aggregation inhibitors, tissue plasminogen activators,urokinase, prourokinase, streptokinase, aspirin and heparin. Thecompounds of this invention can be utilized in vivo, ordinarily inmammals, such as humans, sheep, horses, cattle, pigs, dogs, cats, ratsand mice, or in vitro.

L. Peptide Mimetics.

This invention also includes peptide mimetics which mimic thethree-dimensional structure of Nogo and block Nogo binding at the NgR.Such peptide mimetics may have significant advantages overnaturally-occurring peptides, including, for example: more economicalproduction, greater chemical stability, enhanced pharmacologicalproperties (half-life, absorption, potency, efficacy, etc.), alteredspecificity (e.g., a broad-spectrum of biological activities), reducedantigenicity, and others.

In one form, mimetics are peptide-containing molecules that mimicelements of protein secondary structure. (see, for example, Johnson etal., (1993) Peptide Turn Mimetics, in Biotechnology and Pharmacy,Pezzuto et al., (editors) Chapman and Hall). The underlying rationalebehind the use of peptide mimetics is that the peptide backbone ofproteins exists chiefly to orient amino acid side chains in such a wayas to facilitate molecular interactions, such as those of antibody andantigen. A peptide mimetic is expected to permit molecular interactionssimilar to the natural molecule.

In another form, peptide analogs are commonly used in the pharmaceuticalindustry as non-peptide drugs with properties analogous to those of thetemplate peptide. These types of non-peptide compounds are also referredto as “peptide mimetics” or “peptidomimetics” (Fauchere, (1986) Adv.Drug Res. 15, 29-69; Veber & Freidinger, (1985) Trends Neurosci. 8,392-396; Evans et al., (1987) J. Med. Chem. 30, 1229-1239, which areincorporated herein by reference) and are usually developed with the aidof computerized molecular modeling.

Peptide mimetics that are structurally similar to therapeutically usefulpeptides may be used to produce an equivalent therapeutic orprophylactic effect. Generally, peptide mimetics are structurallysimilar to a paradigm polypeptide (i.e., a polypeptide that has abiochemical property or pharmacological activity), such as theextracellular domain of Nogo, but have one or more peptide linkagesoptionally replaced by a linkage selected from the group consisting of:—CH2NH—, —CH2S—, —CH2-CH2-, —CH═CH— (cis and trans), —COCH2-,—CH(OH)CH2- and —CH2SO—, by methods known in the art and furtherdescribed in the following references; Weinstein, (1983) Chemistry andBiochemistry of Amino Acids, Peptides and Proteins, Marcel Dekker;Morley, (1980) Trends Pharmacol. Sci. 1, 463-468 (general review);Hudson et al., (1979) Int. J. Pept. Protein Res. 14, 177-185 (—CH2NH—,CH2CH2-); Spatola et al., (1986) Life Sci. 38, 1243-1249 (—CH2-S); Hann,(1982) J. Chem. Soc. Perkin Trans. 1, 307-314 (—CH—CH—, cis and trans);Almquist et al., (1980) J. Med. Chem. 23, 1392-1398 (—COCH2-);Jennings-White et al., (1982) Tetrahedron Lett. 23, 2533 (—COCH2-);Holladay et al., (1983) Tetrahedron Lett. 24, 4401-4404 (—C(OH)CH2-);and Hruby, (1982) Life Sci. 31, 189-199 (—CH2S—); each of which isincorporated herein by reference.

Labeling of peptide mimetics usually involves covalent attachment of oneor more labels, directly or through a spacer (e.g., an amide group), tonon-interfering position(s) on the peptide mimetic that are predicted byquantitative structure-activity data and molecular modeling. Suchnon-interfering positions generally are positions that do not formdirect contacts with the macromolecule(s) (e.g., are not contact pointsin Nogo-NgR complexes) to which the peptide mimetic binds to produce thetherapeutic effect. Derivitization (e.g., labeling) of peptide mimeticsshould not substantially interfere with the desired biological orpharmacological activity of the peptide mimetic.

Nogo peptide mimetics can be constructed by structure-based drug designthrough replacement of amino acids by organic moieties (see, forexample, Hughes, (1980) Philos. Trans. R. Soc. Lond. 290, 387-394;Hodgson, (1991) Biotechnol. 9, 19-21; Suckling, (1991) Sci. Prog. 75,323-359).

The use of peptide mimetics can be enhanced through the use ofcombinatorial chemistry to create drug libraries. The design of peptidemimetics can be aided by identifying amino acid mutations that increaseor decrease binding of Nogo at the NgR. Approaches that can be usedinclude the yeast two hybrid method (see Chien et al., (1991) Proc.Natl. Acad. Sci. USA 88, 9578-9582) and using the phage display method.The two hybrid method detects protein-protein interactions in yeast(Fields et al., (1989) Nature 340, 245-246). The phage display methoddetects the interaction between an immobilized protein and a proteinthat is expressed on the surface of phages such as lambda and M13(Amberg et al., (1993) Strategies 6, 2-4; Hogrefe et al., (1993) Gene128, 119-126). These methods allow positive and negative selection forprotein-protein interactions and the identification of the sequencesthat determine these interactions.

For general information on peptide synthesis and peptide mimetics, see,for example; Jones, (1992) Amino Acid and Peptide Synthesis, OxfordUniversity Press; Jung, (1997) Combinatorial Peptide and NonpeptideLibraries: A Handbook, John Wiley; Bodanszky et al., (1993) PeptideChemistry—A Practical Textbook, Springer Verlag.

M. Transgenic Animals

The term “animal” as used herein includes all vertebrate animals, excepthumans. It also includes an individual animal in all stages ofdevelopment, including embryonic and fetal stages. A “transgenic animal”is an animal containing one or more cells bearing genetic informationreceived, directly or indirectly, by deliberate genetic manipulation ata subcellular level, such as by microinjection or infection withrecombinant virus. This introduced DNA molecule may be integrated withina chromosome, or it may be extra-chromosomally replicating DNA. The term“germ cell-line transgenic animal” refers to a transgenic animal inwhich the genetic information was introduced into a germ line cell,thereby conferring the ability to transfer the information to offspring.If such offspring in fact possess some or all of that information, thenthey, too, are transgenic animals. Transgenic animals containing mutant,knock-out, modified genes or gene constructs to over-express orconditionally express a polypeptide encoded by the cDNA sequences of SEQID NO: 1 or 3 or related sequences are encompassed in the invention.

The information may be foreign to the species of animal to which therecipient belongs, foreign only to the particular individual recipient,or genetic information already possessed by the recipient. In the lastcase, the introduced gene may be differently expressed compared to thenative endogenous gene. The genes may be obtained by isolating them fromgenomic sources, by preparation of cDNA from isolated RNA templates, bydirected synthesis, or by some combination thereof.

To be expressed, a coding sequence should be operably linked to aregulatory region. Regulatory regions, such as promoters, may be used toincrease, decrease, regulate or designate to certain tissues or tocertain stages of development the expression of a gene. The promoterneed not be a naturally occurring promoter. The “transgenic non-humananimals” of the invention are produced by introducing “transgenes” intothe germline of the non-human animal. The methods enabling theintroduction of DNA into cells are generally available and well-known inthe art. Different methods of introducing transgenes could be used.Generally, the zygote is the best target for microinjection. In themouse, the male pronucleus reaches the size of approximately twentymicrons in diameter, which allows reproducible injection of one to twopicoliters of DNA solution. The use of zygotes as a target for genetransfer has a major advantage. In most cases, the injected DNA will beincorporated into the host gene before the first cleavage (Brinster etal., (1985) Proc. Natl. Acad. Sci. USA 82, 4438-4442). Consequently,nearly all cells of the transgenic non-human animal will carry theincorporated transgene. Generally, this will also result in theefficient transmission of the transgene to offspring of the foundersince 50% of the germ cells will harbor the transgene. Microinjection ofzygotes is a preferred method for incorporating transgenes in practicingthe invention.

Retroviral infection can also be used to introduce a transgene into anon-human animal. The developing non-human embryo can be cultured invitro to the blastocyst stage. During this time, blastomeres may betargets for retroviral infection. Efficient infection of the blastomeresis obtained by enzymatic treatment to remove the zona pellucida. Theviral vector system used to introduce the transgene is typically areplication-defective retrovirus carrying the transgene (Jahner et al.,(1985) Proc. Natl. Acad. Sci. USA 82, 6927-6931; Van der Putten et al.,(1985) Proc. Natl. Acad. Sci. USA 82, 6148-6152). Transfection is easilyand efficiently obtained by culturing the blastomeres on a monolayer ofvirus-producing cells (Van der Putten et al., (1985) Proc. Natl. Acad.Sci. USA 82, 6148-6152; Stewart et al., (1987) EMBO J. 6, 383-388).Alternatively, infection can be performed at a later stage. Virus orvirus-producing cells can be injected into the blastocoele (Jahner etal., (1982) Nature 298, 623-628). Most of the founder animals will bemosaic for the transgene since incorporation occurs only in a subset ofthe cells which formed the transgenic non-human animal. Furthermore, thefounder animal may contain retroviral insertions of the transgene at avariety of positions in the genome; these generally segregate in theoffspring. In addition, it is also possible to introduce transgenes intothe germ line, albeit with low efficiency, by intrauterine retroviralinfection of the midgestation embryo (Jahner et al., (1982) Nature 298,623-628).

A third type of target cell for transgene introduction is the embryonalstem cell (ES). ES cells are obtained from pre-implantation embryoscultured in vitro (Evans et al., (1981) Nature 292, 154-156; Bradley etal., (1984) Nature 309, 255-256; Gossler et al., (1986) Proc. Natl.Acad. Sci. USA 83, 9065-9069). Transgenes can be efficiently introducedinto ES cells by DNA transfection or by retrovirus-mediatedtransduction. The resulting transformed ES cells can thereafter becombined with blastocysts from a non-human animal. The ES cells colonizethe embryo and contribute to the germ line of the resulting chimericanimal.

The methods for evaluating the presence of the introduced DNA as well asits expression are readily available and well-known in the art. Suchmethods include, but are not limited to DNA (Southern) hybridization todetect the exogenous DNA, polymerase chain reaction (PCR),polyacrylamide gel electrophoresis (PAGE) and Western blots to detectDNA, RNA and protein. The methods include immunological andhistochemical techniques to detect expression of a NgR gene.

As used herein, a “transgene” is a DNA sequence introduced into thegermline of a non-human animal by way of human intervention such as byway of the Examples described below. The nucleic acid sequence of thetransgene, in this case a form of SEQ ID NO: 1 or 3, may be integratedeither at a locus of a genome where that particular nucleic acidsequence is not otherwise normally found or at the normal locus for thetransgene. The transgene may consist of nucleic acid sequences derivedfrom the genome of the same species or of a different species than thespecies of the target animal. For example, axonal regeneration in micelacking Nogo can be compared with that in mice lacking MAG or both MAGand Nogo. To determine if the effect of the anti-Nogo antibody is due toNogo blockade, antibody effects can be studied in animals lacking Nogoexpression.

As discussed above, a nucleic acid of the invention can be transfectedinto a host cell using a vector. Preferred vectors are plasmids andviral vectors, such as retroviruses. Viral vectors may be used toproduce a transgenic animal according to the invention. Preferably, theviral vectors are replication defective, that is, they are unable toreplicate autonomously in the target cell. In general, the genome of thereplication defective viral vectors which are used within the scope ofthe present invention lack at least one region which is necessary forthe replication of the virus in the infected cell. These regions caneither be eliminated (in whole or in part), or be renderednon-functional by any technique known to a person skilled in the art.These techniques include the total removal, substitution (by othersequences, in particular by the inserted nucleic acid), partial deletionor addition of one or more bases to an essential (for replication)region. Such techniques may be performed in vitro (on the isolated DNA)or in situ, using the techniques of genetic manipulation or by treatmentwith mutagenic agents.

Preferably, the replication defective virus retains the sequences of itsgenome which are necessary for encapsidating the viral particles. Theretroviruses are integrating viruses which infect dividing cells. Theretrovirus genome includes two LTRs, an encapsidation sequence and threecoding regions (gag, pol and env). The construction of recombinantretroviral vectors has been described (see, for example, Bernstein etal., (1985) Genet. Eng. 7, 235; McCormick, (1985) Biotechnol. 3,689-691). In recombinant retroviral vectors, the gag, pol and env genesare generally deleted, in whole or in part, and replaced with aheterologous nucleotide sequence of interest. These vectors can beconstructed from different types of retrovirus, such as, HIV, MoMuLV(murine Moloney leukemia virus), MSV (murine Moloney sarcoma virus),HaSV (Harvey sarcoma virus); SNV (spleen necrosis virus); RSV (Roussarcoma virus) and Friend virus.

In general, in order to construct recombinant retroviruses containing anucleotide sequence, a plasmid is constructed which contains the LTRs,the encapsidation sequence and the coding sequence. This construct isused to transfect a packaging cell line, which cell line is able tosupply in trans the retroviral functions which are deficient in theplasmid. In general, the packaging cell lines are thus able to expressthe gag, pol and env genes. Such packaging cell lines have beendescribed in the prior art, in particular the cell line PA317 (U.S. Pat.No. 4,861,719); the PsiCRIP cell line (WO9002806) and the GP+envAm-12cell line (WO8907150). In addition, the recombinant retroviral vectorscan contain modifications within the LTRs for suppressingtranscriptional activity as well as extensive encapsidation sequenceswhich may include a part of the gag gene (Bender et al., (1987) J.Virol. 61, 1639-1646). Recombinant retroviral vectors are purified bystandard techniques known to those having ordinary skill in the art.

In one aspect the nucleic acid encodes antisense RNA molecules. In thisembodiment, the nucleic acid is operably linked to suitable regulatoryregions (discussed above) enabling expression of the nucleotidesequence, and is introduced into a cell utilizing, preferably,recombinant vector constructs, which will express the antisense nucleicacid once the vector is introduced into the cell. Examples of suitablevectors includes plasmids, adenoviruses, adeno-associated viruses (see,for example, U.S. Pat. No. 4,797,368, U.S. Pat. No. 5,139,941),retroviruses (see above), and herpes viruses. For delivery of atherapeutic gene the vector is preferably an adeno-associated virus.

Adenoviruses are eukaryotic DNA viruses that can be modified toefficiently deliver a nucleic acid of the invention to a variety of celltypes. Various serotypes of adenovirus exist. Of these serotypes,preference is given, within the scope of the present invention, to usingtype two or type five human adenoviruses (Ad 2 or Ad 5) or adenovirusesof animal origin (see WO9426914). Those adenoviruses of animal originwhich can be used within the scope of the present invention includeadenoviruses of canine, bovine, murine, ovine, porcine, avian, andsimian origin.

The replication defective recombinant adenoviruses according to theinvention can be prepared by any technique known to the person skilledin the art. In particular, they can be prepared by homologousrecombination between an adenovirus and a plasmid which carries, interalia, the DNA sequence of interest. The homologous recombination iseffected following cotransfection of the said adenovirus and plasmidinto an appropriate cell line. The cell line which is employed shouldpreferably (i) be transformable by the said elements, and (ii) containthe sequences which are able to complement the part of the genome of thereplication defective adenovirus, preferably in integrated form in orderto avoid the risks of recombination. Recombinant adenoviruses arerecovered and purified using standard molecular biological techniques,which are well known to one of ordinary skill in the art.

A number of recombinant or transgenic mice have been produced, includingthose which express an activated oncogene sequence (U.S. Pat. No.4,736,866); express Simian SV 40 T-antigen (U.S. Pat. No. 5,728,915);lack the expression of interferon regulatory factor 1 (IRF-1) (U.S. Pat.No. 5,731,490); exhibit dopaminergic dysfunction (U.S. Pat. No.5,723,719); express at least one human gene which participates in bloodpressure control (U.S. Pat. No. 5,731,489); display greater similarityto the conditions existing in naturally occurring Alzheimer's disease(U.S. Pat. No. 5,720,936); have a reduced capacity to mediate cellularadhesion (U.S. Pat. No. 5,602,307); possess a bovine growth hormone gene(Clutter et al., (1996) Genetics 143, 1753-1760) or are capable ofgenerating a fully human antibody response (Zou et al., (1993) Science262, 1271-1274).

While mice and rats remain the animals of choice for most transgenicexperimentation, in some instances it is preferable or even necessary touse alternative animal species. Transgenic procedures have beensuccessfully utilized in a variety of non-murine animals, includingsheep, goats, chickens, hamsters, rabbits, cows and guinea pigs (seeAigner et al., (1999) Biochem. Biophys. Res. Commun. 257, 843-850;Castro et al., (1999) Genet. Anal. 15, 179-187; Brink et al., (2000)Theriogenology 53, 139-148; Colman, (1999) Genet. Anal. 15, 167-173;Eyestone, (1999) Theriogenology 51, 509-517; Baguisi et al., (1999) Nat.Biotechnol. 17, 456-461; Prather et al., (1999) Theriogenology 51,487-498; Pain et al., (1999) Cells Tissues Organs 165, 212-219;Fernandez et al., (1999) Indian J. Exp. Biol. 37, 1085-1092; U.S. Pat.No. 5,908,969; U.S. Pat. No. 5,792,902; U.S. Pat. No. 5,892,070; U.S.Pat. No. 6,025,540).

N. Diagnostic Methods

One means of diagnosing a demyelinating disease using the nucleic acidmolecules or proteins of the invention involves obtaining a tissuesample from living subjects. Obtaining tissue samples from livingsources is problematic for tissues such as those of the central nervoussystem. In patients suffering from a demyelinating disease, tissuesamples for diagnostic methods may be obtained by less invasiveprocedures. For example, samples may be obtained from whole blood andserum.

The use of molecular biological tools has become routine in forensictechnology. For example, nucleic acid probes may be used to determinethe expression of a nucleic acid molecule comprising all or at leastpart of the sequences of SEQ ID NO: 1 in forensic pathology specimens.Further, nucleic acid assays may be carried out by any means ofconducting a transcriptional profiling analysis. In addition to nucleicacid analysis, forensic methods of the invention may target the proteinencoded by SEQ ID NO: 1 to determine up- or down-regulation of the genes(Shiverick et al., (1975) Biochim. Biophys. Acta 393, 124-133).

Methods of the invention may involve treatment of tissues withcollagenases or other proteases to make the tissue amenable to celllysis (Semenov et al., (1987) Biull. Eksp. Biol. Med. 104, 113-116).Further, it is possible to obtain biopsy samples from different regionsof the brain for analysis.

Assays to detect nucleic acid or protein molecules of the invention maybe in any available format. Typical assays for nucleic acid moleculesinclude hybridization or PCR based formats. Typical assays for thedetection of proteins, polypeptides or peptides of the invention includethe use of antibody probes in any available format such as in situbinding assays, etc. See Harlow & Lane, (1988) Antibodies—A LaboratoryManual, Cold Spring Harbor Laboratory Press. In preferred embodiments,assays are carried out with appropriate controls.

Without further description, it is believed that one of ordinary skillin the art can, using the preceding description and the followingillustrative examples, make and utilize the compounds of the presentinvention and practice the claimed methods. The following workingexamples therefore, specifically point out preferred embodiments of thepresent invention, and are not to be construed as limiting in any waythe remainder of the disclosure.

Key for Sequence Listing SEQ ID NO: Description SEQ ID NO: 1 human NgRnucleotide sequence SEQ ID NO: 2 human NgR amino acid sequence SEQ IDNO: 3 mouse NgR nucleotide sequence SEQ ID NO: 4 mouse NgR amino acidsequence SEQ ID NO: 5 human NogoA nucleotide sequence SEQ ID NO: 6 humanNogoA amino acid sequence SEQ ID NO: 7 a nucleotide sequence coding foramino acid residues #1054-1078 of a human NogoA SEQ ID NO: 8 amino acidresidues #1064-1088 of human NogoA SEQ ID NO: 9 a nucleotide sequencecoding for amino acid residues #1064-1088 of a human NogoA SEQ ID NO: 10amino acid residues #1064-1088 of human NogoA SEQ ID NO: 11 a nucleotidesequence coding for amino acid residues #1064-1088 of a human NogoA SEQID NO: 12 amino acid residues #1064-1088 of a human NogoA SEQ ID NO: 13a nucleotide sequence coding for amino acid residues #1084-1108 of ahuman NogoA SEQ ID NO: 14 amino acid residues #1084-1108 of a humanNogoA SEQ ID NO: 15 a nucleotide sequence coding for amino acid residues#1095-1119 of a human NogoA SEQ ID NO: 16 amino acid residues #1095-1119of a human NogoA SEQ ID NO: 17 a nucleotide sequence coding for aminoacid residues #1055-1094 of a human NogoA SEQ ID NO: 18 amino acidresidues #1055-1094 of a human NogoA SEQ ID NO: 19 a nucleotide sequencecoding for amino acid residues #1054-1119 of a human NogoA SEQ ID NO: 20amino acid residues #1054-1119 of a human NogoA SEQ ID NO: 21 anucleotide sequence coding for amino acid residues #1055-1120 of a humanNogoA SEQ ID NO: 22 amino acid residues #1055-1120 of a human NogoA SEQID NO: 23 a nucleotide sequence coding for amino acid residues#1055-1079 of a human NogoA SEQ ID NO: 24 amino acid residues #1055-1079of a human NogoA SEQ ID NO: 25 a nucleotide sequence coding for aminoacid residues #1055-1084 of a human NogoA SEQ ID NO: 26 amino acidresidues #1055-1084 of a human NogoA SEQ ID NO: 27 a nucleotide sequencecoding for amino acid residues #1055-1089 of a human NogoA SEQ ID NO: 28amino acid residues #1055-1089 of a human NogoA SEQ ID NO: 29 anucleotide sequence coding for amino acid residues #1060-1094 of a humanNogoA SEQ ID NO: 30 amino acid residues #1060-1094 of a human NogoA SEQID NO: 31 a nucleotide sequence coding for amino acid residues#1065-1094 of a human NogoA SEQ ID NO: 32 amino acid residues #1065-1094of a human NogoA SEQ ID NO: 33 a nucleotide sequence coding for aminoacid residues #1070-1084 of a human NogoA SEQ ID NO: 34 amino acidresidues #1070-1084 of a human NogoA SEQ ID NO: 35 a nucleotide sequencecoding for amino acid residues #1085-1109 of a human NogoA SEQ ID NO: 36amino acid residues #1085-1109 of a human NogoA SEQ ID NO: 37 ΔLRR-NT5′primer SEQ ID NO: 38 NgR3X primer SEQ ID NO: 39 MycNgR305 primer SEQ IDNO: 40 MycNgR primer SEQ ID NO: 41 2NgRt313 primer SEQ ID NO: 42TM/GPI5′ primer SEQ ID NO: 43 DEL LRR1 primer SEQ ID NO: 44 DEL LRR2primer SEQ ID NO: 45 DEL LRR3 primer SEQ ID NO: 46 DEL LRR4 primer SEQID NO: 47 DEL LRR5 primer SEQ ID NO: 48 DEL LRR6 primer SEQ ID NO: 49DEL LRR7 primer SEQ ID NO: 50 DEL LRR8 primer SEQ ID NO: 51 3DLRR CTprimer SEQ ID NO: 52 5 DLRRCT primer SEQ ID NO: 53 amino acid residues#306-442 of a human NgR SEQ ID NO: 54 amino acid residues #306-473 of ahuman NgR SEQ ID NO: 55 amino acid residues #27-309 of a human NgR SEQID NO: 56 synthetic peptide SEQ ID NO: 57 synthetic peptide

EXAMPLES Example 1—Identification of Nogo as a Member of the ReticulonFamily of Proteins

Adult mammalian axon regeneration is generally successful in theperiphery but dismally poor in the CNS. However, many classes of CNSaxons can extend for long distances in peripheral nerve grafts (Benfy &Aguayo (1982) Nature 296, 150-152). Comparison of CNS and peripheralnervous system (PNS) myelin has revealed that CNS white matter isselectively inhibitory for axonal outgrowth (Schwab & Thoenen (1985) J.Neurosci. 5, 2415-2423). Several components of CNS white matter, NI35,NI250 (Nogo) and MAG, with inhibitory activity for axon extension havebeen described (Wang et al., (1999) Transduction of inhibitory signalsby the axonal growth cone, in Neurobiology of Spinal Cord Injury, Kalb &Strittmatter (editors) Humana Press; Caroni & Schwab, (1988) J. CellBiol. 106, 1281-1288; Spillmann et al., (1998) J. Biol. Chem. 73,19283-19293; McKerracher et al., (1994) Neuron 13, 805-811; Mukhopadhyayet al., (1994) Neuron 13, 757-767.) The IN-1 antibody raised againstNI35 and NI250 (Nogo) has been reported to allow moderate degrees ofaxonal regeneration and functional recovery after spinal cord injury(Bregman et al., (1995) Nature 378, 498-501; Thallmair et al., (1998)Nature Neurosci. 1, 24-31). The present invention identifies Nogo as amember of the Reticulon protein family.

Nogo is expressed by oligodendrocytes but not by Schwann cells, andassociates primarily with the endoplasmic reticulum. The 66 amino acidlumenal-extracellular domain of Nogo (SEQ ID NO: 20) inhibits axonalextension and collapses dorsal root ganglion growth cones. OtherReticulon proteins are not expressed by oligodendrocytes, and the 66amino acid lumenal-extracellular domain from other Reticulon proteinsdoes not inhibit axonal regeneration. These data provide a molecularbasis to assess the contribution of Nogo to the failure of axonalregeneration in the adult CNS.

For expression and protein purification of recombinant Nogo-A, the fulllength sequence (KIAA0886) was generously provided by the Kazusa DNAResearch Institute. The full length coding sequence was amplified by thepolymerase chain reaction (PCR) and ligated into the pCDNA3.1-MycHisvector (Invitrogen) to generate a plasmid encoding Nogo-A fused at thecarboxyl terminus to the Myc epitope (Nogo-A-Myc). Alternatively, thecoding sequence was amplified using primers that encode an in-frame Mycepitope immediately amino terminal to the first residue and a stop codonat the carboxyl terminus (Myc-Nogo-A). The Nogo-C-MycHis andRtn1C-MycHis expression vectors were derived in the same fashion exceptthat an adult rat brain cDNA library was used as template for a PCRreaction with primers was based on the Nogo-C or Rtn1C sequences (Van deVelde et al., (1994) J. Cell. Sci. 107, 2403-2416). These plasmids weretransfected into COS-7 or HEK293T by the Lipofectamine (Gibco-BRL) orthe FuGENE 6 (Boerhinger Mannheim) method.

A portion of Nogo-A encoding the 66 amino acid lumenal-extracellularfragment of Nogo-A was amplified by PCR and ligated into the pGEX-2Tplasmid to yield a prokaryotic expression vector for the GST-Nogo fusionprotein. Similar regions of Rtn1, Rtn2 and Rtn3 were amplified by nestedPCR using an adult rat brain cDNA library as template and ligated topGEX-2T. E. coli transformed with these plasmids were induced with IPTG.Soluble, native GST fusion proteins were purified using aglutathione-resin and contained approximately 75% GST and 25% fulllength GST-Nogo or GST-Rtn protein. The majority of the GST-Nogo proteinwas not extractable from under non-denaturing conditions, but an 8 Murea extract dialyzed against PBS contained over 98% pure GST-Nogo.

Myc immunoreactivity is detectable with an apparent size in the 225 kDarange under reducing conditions (data not shown). Thus, the cDNA directsthe expression of a protein with appropriate electrophoretic mobilityand the amino acid sequence to be Nogo which was termed human Nogo-A(hNogo-A).

The conserved carboxyl tail of the Rtn family proteins contains twohydrophobic domains separated by a 66 amino acid residue hydrophilicsegment. None of the sequences contain a signal peptide. The predictedtopology for these proteins is for the amino and carboxyl termini toreside in the cytosol, and for the conserved region to associate withthe lipid bilayer. For Rtn1-A, there is experimental evidencedemonstrating that the polypeptide behaves as an integral membraneprotein, and that the hydrophobic segments of the conserved domain areresponsible for this behavior (Van de Velde et al., (1994) J. Cell. Sci.107, 2403-2416). Myc-tagged Nogo is also associated with particulatefractions and is extracted by detergent but not high ionic strength(data not shown).

When overexpressed in kidney cells, the Rtn1 protein is localizedprimarily to endoplasmic reticulum (ER) in a finely granulated pattern,hence the Reticulon name (Van de Velde et al., (1994) J. Cell. Sci. 107,2403-2416). There is a di-lysine ER retention motif at the carboxylterminus of Nogo and most Rtn proteins (Van de Velde et al., (1994) J.Cell. Sci. 107, 2403-2416; Jackson et al., (1991) EMBO J. 9, 3153-3162).In neurons, Rtn1 is expressed throughout processes and is concentratedin growth cones (Senden et al., (1996) Eur. J. Cell. Biol. 69, 197-213).Its localization in transfected kidney cells has led to the suggestionthat Rtn1 might regulate protein sorting or other aspects of ER function(Van de Velde et al., (1994) J. Cell. Sci. 107, 2403-2416). Both the Aand C splice forms of Nogo exhibit a reticular distribution whenexpressed in COS-7 cells, similar to that of Rtn1-C.

Example 2—Polyclonal Antibodies Against Nogo

The predicted intra-membrane topology of the two hydrophobic domains ofNogo indicates that the 66 amino acid residues between these segments islocalized to the lumenal/extracellular face of the membrane. To explorethis further, an antiserum directed against the 66 amino acid domain wasgenerated.

For antibody production and immunohistology, anti-Myc immunoblots andimmunohistology with the 9E10 antibody were obtained as described inTakahashi et al., (1998) Nature Neurosci., 1, 487-493 & Takahashi etal., (1999) Cell, 99, 59-69. The GST-Nogo fusion protein was employed asan immunogen to generate an anti-Nogo rabbit antiserum. Antibody wasaffinity-purified and utilized at 3 μg/ml for immunohistology and 1μg/ml for immunoblots. To assess the specificity of the antiserum,staining was conducted in the presence of GST-Nogo protein at 0.1 mg/ml.For live cell staining, cells were incubated in primary antibodydilutions at 4° C. for one hour in Hanks balanced salt solution with0.05% BSA and 20 mM Na-Hepes (pH 7.3). After fixation, bound antibodywas detected by incubation with fluorescently labeled secondaryantibodies.

The antibody detects a low level of surface expression of this epitope,while the Myc epitope at the carboxyl terminus of expressed Nogo is notdetected unless cells are permeablized. This surface staining wasattributed to a minority of Nogo protein associated with the plasmamembrane rather than the ER membrane. This data supports a topographicmodel wherein the amino and carboxyl termini of the protein reside inthe cytoplasm and 66 amino acid of the protein protrude on thelumenal-extracellular side of the ER or plasma membrane.

Example 3—Nogo Expression in the Central Nervous System

If Nogo is a major contributor to the axon outgrowth inhibitorycharacteristics of CNS myelin as compared to PNS myelin (Caroni &Schwab, (1988) J. Cell Biol. 106, 1281-1288; Spillmann et al., (1998) J.Biol. Chem. 73, 19283-19293; Bregman et al., (1995) Nature 378,498-501), then Nogo should be expressed in adult CNS myelin but not PNSmyelin. Northern blot analysis of Nogo expression was performed usingprobes derived from the 5′ Nogo-AB-specific region and from the 3′ Nogocommon region of the cDNA. A single band of about 4.1 kilobase wasdetected with the 5′ probe in adult rat optic nerve total RNA samples,but not sciatic nerve samples. The results indicate that the Nogo-Aclone is a full length cDNA, and are consistent with a role for Nogo asa CNS-myelin-specific axon outgrowth inhibitor. Northern blot analysiswith a 3′ probe reveals that optic nerve expresses high levels of theNogo-A mRNA and much lower levels of Nogo-B and Nogo-C. Whole brainexpresses both Nogo-A and Nogo-C, but a number of peripheral tissues(including sciatic nerve) express little or no Nogo. Nogo-C/Rtn4-Cexpression has been demonstrated in skeletal muscle and adipocytes, aswell as in brain (Morris et al., (1991) Biochim. Biophys. Acta 1450,68-76). Within the Rtn family, optic nerve expression appears to beselective for Nogo, with no detectable expression of Rtn 1 or Rtn 3. Rtn2 has not been examined.

In situ hybridization reveals Nogo mRNA in cells with the morphology ofoligodendrocytes in adult rat optic nerve and pyramidal tract. Withinthe brain, Nogo expression is also detected in certain neuronalpopulations. In contrast to Nogo, Rtn1 and Rtn3 are not expressed inoptic nerve but mRNA is detected in certain neuronal populations. Nogoprotein localization was analyzed in spinal cord cultures treated withPDGF and low serum to induce oligodendrocyte differentiation, using theanti-Nogo antibody and the oligodendrocyte-specific O4 monoclonalantibody. In living cells, both the lumenal-extracellular 66 amino acidloop of Nogo and the O4 antigen are detected on the surface ofoligodendrocytes. Approximately half of O4-positive cells in thesecultures exhibit Nogo surface staining.

Example 4—Nogo-Mediated Growth Cone Collapse

For all experiments involving cell culture, the following methods wereemployed. The culture of embryonic chick E10 and E12 dorsal rootganglion explants and dissociated neurons utilized methods described forE7 dorsal root ganglion cultures (Takahashi et al., (1998) NatureNeurosci. 1, 487-493; Takahashi et al., (1999) Cell 99, 59-69; Goshimaet al., (1995) Nature 376, 509-514; Jin & Strittmatter, (1997) J.Neurosci. 7, 6256-6263). NGF-differentiated PC12 cells were cultured asdescribed (Strittmatter et al., (1994) J. Neurosci. 14, 2327-2338).Embryonic spinal cord explants (rat E10 or chick E5) were cultured for7-14 days in the presence of PDGF-AA to induce differentiation of somecells into mature oligodendrocytes (Vartanian et al., (1999) Proc. Natl.Acad. Sci. USA 96, 731-735). The procedure for growth cone collapseassays is identical to that for analysis of Sema3A-induced growth conecollapse (Takahashi et al., (1998) Nature Neurosci. 1, 487-493;Takahashi et al., (1999) Cell 99, 59-69; Goshima et al., (1995) Nature376, 509-514; Jin & Strittmatter, (1997) J. Neurosci. 17, 6256-6263).The method for analysis of total neurite outgrowth has also beendescribed (Goshima et al., (1995) Nature 376, 509-514; Jin &Strittmatter, (1997) J. Neurosci. 17, 6256-6263; Strittmatter et al.,(1994) J. Neurosci. 14, 2327-2338). In outgrowth assays, proteins andpeptides were added one hour after plating to minimize any effect on thetotal number of adherent cells. To test the effect of substrate-boundGST or GST-Nogo, the protein solutions were dried on poly-L-lysinecoated glass, washed and then coated with laminin. For E12 cultures, theneuronal identity of cells was verified by staining withanti-neurofilament antibodies (2H3, Developmental Studies HybridomaBank) and neurites were traced by observation of rhodamine-phalloidinstaining of F-actin in processes.

The expression of recombinant Nogo in HEK293T cells allows a rigoroustest of whether this protein has axon outgrowth inhibiting effects.Washed membrane fractions from vector- or hNogo-A-Myc-transfectedHEK293T cells were added to chick E12 dorsal root ganglion explantcultures. Growth cone morphology was assessed after a thirty minuteincubation at 37° C. by fixation and rhodamine-phalloidin staining.

The control HEK membranes have no detectable effect on growth conemorphology. The Nogo-A-containing membrane fractions induced collapse ofa majority of dorsal root ganglion growth cones. This growth conecollapse indicates an axon outgrowth inhibiting activity, and Nogoinhibition of axon extension is also demonstrable (see below). TheNogo-C form also exhibits collapse activity, indicating that the sharedcarboxyl terminus of the protein including the hydrophobic segments andthe 66 amino acid lumenal-extracellular domain contains functionallyimportant residues. Additional inhibitory activity in the amino terminalregion of Nogo-A is not excluded by these studies. The sensitivity ofmore immature explant cultures from E10 chick embryos or from E15 ratembryos (data not shown) is substantially less. The developmentalregulation of sensitivity is consistent with experiments using partiallypurified Nogo (Bandtlow et al., (1997) Eur. J. Neurosci. 9, 2743-2752).

Within the growth cone collapsing Nogo-C protein, the hydrophilic 66lumenal-extracellular domain seems more likely to interact with thesurface of dorsal root ganglion neurons than do the membrane-embeddedhydrophobic domains. To test this hypothesis, the 66 amino acid regionof hNogo was expressed in and purified from E. coli. A majority of theGST-Nogo fusion protein accumulates in inclusion bodies, but can berecovered by urea extraction. This restricted region of Nogo possessespotent (EC50=50 nM) growth cone collapsing activity for chick E12 dorsalroot ganglion neurons (data not shown). The urea-extracted proteinpreparation is likely to present only a small fraction of the Nogosequence in an active conformation. Therefore, 10% of GST-Nogo that issoluble in E. coli was purified using a glutathione-Sepharose resin.This preparation is even more potent than the urea-extracted protein asa collapsing factor, acutely altering growth cone morphology atconcentrations as low as 1 nM.

The nanomolar potency is on a par with most known physiologic regulatorsof axon guidance. Axon outgrowth from dorsal root ganglion neurons andNGF-differentiated PC12 cells is also blocked by this soluble GST-Nogoprotein in nM concentrations (data not shown). When GST-Nogo is bound tosubstrate surfaces, axonal outgrowth from dorsal root ganglion neuronsor PC12 cells is reduced to undetectable levels. These are selectiveeffects on axon outgrowth rather than cell survival since GST-Nogo doesnot reduce the number of neurofilament-positive adherent cells (137±24%of GST-treated cultures) nor significantly alter the number of apoptoticnuclei identified by DAPI staining (4.0±1.7% in control cultures and5.2±1.1% in GST-Nogo-treated specimens).

Oligodendrocytes appear to express Nogo selectively amongst the Rtnproteins. To explore the selectivity of Nogo s role in the inhibition ofaxonal regeneration, the axon outgrowth inhibiting activity of other Rtnproteins was considered. The predicted lumenal-extracellular 66 aminoacid fragments of Rtn1, Rtn2 and Rtn3 were expressed as GST fusionproteins and purified in native form. At concentrations in which theNogo fragment collapses a majority of E12 dorsal root ganglion growthcones, the other Rtn proteins do not alter growth cone morphology (datanot shown). Thus, the axon regeneration inhibiting activity is specificfor Nogo in the Rtn family.

Example 5—NgR Peptide Agents

To further define the active domain of Nogo, 25 amino acid residuepeptides corresponding to segments of the 66 amino acid sequence weresynthesized. The peptide corresponding to residues 31-55 of theextracellular fragment of Nogo exhibits growth cone collapsing (FIG. 2B)and outgrowth inhibiting (data not shown) activities at concentrationsof 4 μM. While this sequence may provide the core of the inhibitorydomain, the 66 amino acid fragment is clearly required for full potency.Interestingly, this is the region within the 66 amino acid domainsharing the least similarity to other Rtn proteins, consistent with theother family members being inactive as axon regeneration inhibitors.Indeed, the Rtn1 31-55 amino acid lumenal-extracellular peptide exertsno growth cone collapse activity (data not shown).

The aforementioned experimental data identifies Nogo as anoligodendrocyte-specific member of the Rtn family and demonstrates thata discrete domain of Nogo can inhibit axon outgrowth. Other Rtn proteinsdo not possess this activity. The expression of Nogo in oligodendrocytesbut not Schwann cells therefore contributes to the failure of axonalregeneration in the adult mammalian CNS as compared to the adult PNS.The relative contribution of Nogo as compared to other CNS myelincomponents to the non-permissive nature of CNS white matter can now becharacterized at a molecular level.

While the current experimental data is consistent with a role for Nogoin blocking adult CNS axonal regeneration after pathologic injury, thismay also be related to the physiologic role of Nogo in non-pathologicstates. Based on localization studies, other Rtn proteins are thought toplay a role in ER function (Van de Velde et al., (1994) J. Cell. Sci.107, 2403-2416). A majority of Nogo is distributed in a reticularpattern in COS-7 cells and only a minority seems to be accessible at thecell surface.

Example 6—Inhibition of Nogo Activity

The previous examples have shown that a 66 amino acid region near thecarboxyl terminus of Nogo inhibits axon outgrowth and is expressed atthe cell surface. Shorter twenty-five amino acid segments of this domainare either inert as outgrowth inhibitors or of much lower potency(GrandPré et al., (2000) Nature 403, 439-444). The 31-55 region fromthis 66 amino acid segment has weak growth cone collapse and axonoutgrowth inhibiting activity. To block Nogo action in vivo, acompetitive antagonist of Nogo which binds to the same receptor site butdoes not exert a biological effect in its own right would be highlydesirable. Various fragments of the 66 amino acid region were tested asblockers of Nogo-mediated axon growth inhibition. Two assays have beenused for this purpose. The first is the growth cone collapse assay andthe second is a binding assay.

In the growth cone collapse assay, the response to Nogo was measured inthe presence of various potential antagonistic peptides. Three of thetwenty-five amino acid peptides (1-25, 11-35 and 21-45) from the 66amino acid region possess blocking activity at μM concentrations (FIG.2B). The combination of all three peptides does not alter growth conemorphology under basal conditions but totally prevents collapse by 15 nMGST-Nogo. The same mixture of peptides is also capable of blocking lowdose CNS myelin induced growth cone collapse. This blockade supports thehypothesis that Nogo is a primary inhibitory component of CNS myelin.Furthermore, the blockade has properties expected for competitiveantagonism, being ineffective at high doses of CNS myelin.

To develop an antagonist with higher specificity and potency, a longerfragment of Nogo has been tested. Preferentially, such a peptide itselfhas no axon outgrowth inhibiting activity on its own while competitivelyblocking Nogo action. The 2-41 fragment of Nogo is acetylated at thecarboxy terminus and amidated at the amino terminous and is the highestpotency blocker of Nogo defined to date. Pep2-41 abolishesGST-Nogo-induced growth cone collapse and possesses an apparent Ki of150 nM in the binding assay (FIGS. 3A and 3B). The 2-41 fragment alsoblocks the ability of both purified Nogo-66 protein and crude CNS myelinto inhibit neurite outgrowth in cultured neurons (FIGS. 4A and 4B).

Example 7—Identification of the NgR

A Nogo binding assay was developed which utilizes a method widely usedin examining semaphorin and ephrin axonal guidance function (Flanagan &Vanderhaeghen, (1998) Annu. Rev. Neurosci. 21, 309-345; Takahashi etal., (1999) Cell 99, 59-69). It involves fusing a secreted placentalalkaline phosphatase (AP) moiety to the ligand in question to provide abiologically active receptor binding agent which can be detected with anextremely sensitive colorimetric assay. For Nogo, an expression vectorwas created encoding a signal peptide, a His6 tag for purification, APand the 66 amino acid active domain of Nogo. The fusion protein can bepurified from the conditioned medium of transfected cells in milligramamounts (FIG. 5A). This protein is biologically active as a growth conecollapsing agent, with an EC50 of 1 nM. AP-Nogo is actually slightlymore potent than GST-Nogo perhaps because the protein is synthesized ineukaryotic rather than a prokaryotic cell. Initial studies have revealedsaturable, high affinity sites on axons. Binding is blocked by GST-Nogoand by the antagonistic 25 amino acid peptides, consistent withcompetitive binding to a neuronal receptor site. Since the apparent Kd(3 nM) for these sites in close to the EC50 of AP-Nogo in the collapseassay, the sites are likely to be physiologically relevant NgRs.

This assay was utilized for expression cloning of a NgR. Pools of amouse adult brain cDNA expression library representing 250,000independent clones were transfected into non-neuronal COS-7 cells.Non-transfected COS-7 cells do not bind AP-Nogo, but transfection withtwo pools of 5,000 clones exhibited a few cells with strong AP-Nogobinding. Single cDNA clones encoding a Nogo biding site were isolated bysib-selection from each of the two positive pools. The two independentlyisolated clones are identical to one another except for a 100 bpextension of the 5′ untranslated region in one clone. Transfection ofthese clones into COS-7 cells yields a binding site with an affinity forAP-Nogo identical to that observed in E13 dorsal root ganglion neurons;the Kd for binding is about 3 nM (FIG. 6). AP alone does not bind withany detectable affinity to these transfected cells, indicating that theaffinity is due to the 66 amino acid derived from Nogo. Furthermore,GST-Nogo displaces AP-Nogo from these sites.

This cDNA encodes a novel 473 amino acid protein. There is no reportedcDNA with significant homology in GenBank. The predicted proteincontains a signal peptide followed by eight leucine-rich repeat regions,a unique domain and a predicted GPI anchorage site (FIG. 7). A humanhomologue of the murine cDNA was identified that shares 89% amino acididentity. The existence of this cDNA was predicted from the murine cDNAstructure and analysis of human genomic sequence deposited in GenBank aspart of the Human Sequencing Project. The exons of the human cDNA aredistributed over 35 kilobases and the cDNA was not previously recognizedin the genomic sequence. The protein structure is consistent with a cellsurface protein capable of binding Nogo. The GPI-linked nature of theprotein suggests that there may be a second receptor subunit that spansthe plasma membrane and mediates Nogo signal transduction.

Example 8—Tissue Distribution of NgR

The distribution of the mRNA for this NgR is consistent with a role forthe protein in regulating axonal regeneration and plasticity in theadult CNS. Northern analysis shows a single band of 2.3 kilobases in theadult brain, indicating that the isolated NgR clone is full length (FIG.8). Low levels of this mRNA are observed in heart and kidney but not inother peripheral tissues. In the brain, expression is widespread andthose areas richest in gray matter express the highest levels of themRNA.

Example 9—Biological Effects of Different Nogo Domains

Assays of Nogo-A function have included growth cone collapse, neuriteoutgrowth, and fibroblast spreading with substrate-bound and solubleprotein preparations (Caroni & Schwab, (1988) J. Cell Biol. 106,1281-1288; GrandPré et al., (2000) Nature 403, 439-444; Chen et al.,(2000) Nature 403, 434-439; Prinjha et al., (2000) Nature 403, 483-484).In assays of 3T3 fibroblast morphology, substrate-bound Nogo-66 does notinhibit spreading (FIGS. 1B and 1E). Since NI250 preparations and fulllength Nogo-A are non-permissive for 3T3 spreading, it was necessary toconsider whether different domains of Nogo might subserve this in vitroactivity. To facilitate a comparison of different Nogo-A domains, theacidic amino terminal 1040 amino acid fragment (Amino-Nogo) wasexpressed as a Myc-his tagged protein in HEK293T cells (FIG. 1D). TheNogo protein is present in cytosolic fractions. Surfaces coated withpurified Amino-Nogo protein fail to support 3T3 fibroblast spreading(FIGS. 1B and 1E). Similar results were observed for a kidney-derivedcell line, COS-7 (FIG. 1F). Therefore, the amino terminal domain appearsto account for the effects of full-length Nogo-A on fibroblasts. TheNogo-66 domain is specific for neurons; it does not affect non-neuronalcells.

Dorsal root ganglion cultures were also exposed to Amino-Nogo protein(FIGS. 1C, 1G-1I). As for 3T3 fibroblasts, the fibroblast-like cells inthe dorsal root ganglion culture do not spread on this substrate.Furthermore, axonal outgrowth is reduced to low levels on Amino-Nogocoated surfaces. Thus, while the Nogo-66 effects are neural-specific,the inhibitory action of the Amino-Nogo domain is more generalized. Whenpresented in soluble form at 100 nM, the Nogo-66 polypeptide collapseschick E12 dorsal root ganglion growth cones and nearly abolishes axonalextension, as described previously (GrandPré et al., (2000) Nature 403,439-444). In marked contrast, the soluble Amino-Nogo protein appearsinactive, and does not significantly modulate dorsal root gangliongrowth cone morphology or dorsal root ganglion axonal extension ornon-neuronal cell spreading (FIGS. 1C, 1G-1I).

In the experiments of Walsh and colleague (Prinjha et al., (2000) Nature403, 483-484), cerebellar granule neurons were studied and solubleAmino-Nogo was presented as an Fc fusion protein, presumably in dimericform. Therefore, it was necessary to consider whether these differencesmight explain the inactivity of soluble Amino-Nogo. Mouse P4 cerebellargranule neurons respond to Nogo preparations is a fashionindistinguishable from chick E13 dorsal root ganglion neurons (FIG. 1I).Amino-Nogo dimerized with anti-Myc antibody inhibits 3T3 and COS-7spreading (FIGS. 1E and 1F) and tends to reduce cerebellar axonoutgrowth (FIG. 1I). When further aggregated by the addition ofanti-Mouse IgG antibody, Amino-Nogo significantly reduces both dorsalroot ganglion and cerebellar axon outgrowth (FIGS. 1H and 1I). While theAmino-Nogo protein is quite acidic, electrostatic charge alone does notaccount for its inhibitory effects since poly-Asp does not alter cellspreading or axonal outgrowth (FIGS. 1E, 1F, and 1H). Thus, the Nogo-66domain is a potent and neuron-specific inhibitor, while theintracellular Amino-Nogo domain inhibits multiple cell types and appearsto function only in an aggregated state.

Example 10—Localization of NgR

To further characterize the expression of the Nogo-66 receptor proteinan antiserum to a GST-NgR fusion protein was developed. This antiserumdetects an 85 kDa protein selectively in Nogo-66 receptor-expressingHEK293T cells (FIG. 9A), and specifically stains COS-7 cells expressingNogo-66 receptor (FIG. 9B). Immunohistologic staining of chick embryonicspinal cord cultures localizes the protein to axons, consistent withmediation of Nogo-66-induced axon outgrowth inhibition. Nogo-66 receptorexpression is not found in the O4-positive oligodendrocytes that expressNogo-66. Immunoreactive 85 kDa protein is expressed inNogo-66-responsive neuronal preparations from chick E13 dorsal rootganglion, but to a much lesser degree in weakly responsive tissue fromchick E7 dorsal root ganglion and chick E7 retina (FIG. 9A). Overall,the pattern of Nogo-66 expression is consistent with the proteinmediating Nogo-66 axon inhibition.

This antibody is also effective in localizing the Nogo-66 receptorprotein in tissue sections (FIG. 9C). While it is clear from in situhybridization studies that the protein is expressed in multiple classesof neurons, immunohistology reveals the protein at high levels in CNSwhite matter in profiles consistent with axons. Protein is detectable atlower levels in neuronal soma and neuropil. This provides furthersupport for the proposed function of this protein in mediatinginteractions with oligodendrocytes.

Example 11—NgR Mediates Nogo-66 Responses

The Nogo-66 receptor protein is necessary for Nogo-66 action and notsimply a binding site with a function unrelated to inhibition of axonaloutgrowth. A first prediction is that phosphoinositolspecific-Phospholipase C (PI-PLC) treatment to removeglycophosphatidylinositol (GPI)-linked proteins from the neuronalsurface will render neurons insensitive to Nogo-66. This predictionholds true for chick E13 dorsal root ganglion neurons; PI-PLC treatmentabolishes both AP-Nogo binding and GST-Nogo-66-induced growth conecollapse (FIGS. 10A-10C). As a control, Sema3A responses in the parallelcultures are not altered by PI-PLC treatment. Of course, PI-PLCtreatment is expected to remove a number of proteins from the axonalsurface so this result leaves open the possibility that other GPI-linkedproteins are mediating the Nogo-66 response in untreated cultures.

To demonstrate that the Nogo-66 receptor is capable of mediating Nogo-66inhibition of axon outgrowth, the protein was expressed in neuronslacking a Nogo-66 response. Both dorsal root ganglion and retinalneurons from E7 chick embryos were examined. The Nogo responses in thedorsal root ganglion neurons from this developmental stage are weak butslight responses can be detected in some cultures (data not shown). E7retinal ganglion cell growth cones are uniformly insensitive toNogo-66-induced growth cone collapse (FIG. 10E), do not bind AP-Nogo(data not shown) and do not exhibit 85 kDa anti-Nogo-66 receptorimmunoreactive protein (FIG. 9A). Expression of NgR in these neurons byinfection with recombinant HSV preparations renders the retinal ganglioncell axonal growth cones sensitive to Nogo-66-induced collapse.Infection with a control PlexinA1-expressing control HSV preparationdoes not alter Nogo responses. Taken together, these data indicate thatthe NgR identified here participates in Nogo-66 inhibition of axonregeneration.

Example 12—Structural Analysis of Nogo-66 Receptor

The Nogo-66 receptor structure was examined to determine which regionsmediate Nogo-66 binding. The protein is simply divided into the leucinerich repeat and the non-leucine rich repeat region. Deletion analysisclearly shows that the leucine rich repeats are required for Nogo-66binding but the remainder of the protein is not necessary (FIGS. 11A and11B). Within the leucine rich repeat domain, two domains have beenseparately deleted. This is predicted to maintain the overall leucinerich repeat domain structure, and a similar approach has been utilizedfor the leutropin receptor. It is apparent that the Nogo-66 bindingrequires all eight leucine rich repeats, and suggests that a significantsegment of the planar surface created by the linear beta sheets of theleucine rich repeats. The leucine rich repeat-amino terminous andleucine rich repeat-carboxy terminous conserved cysteine rich regions ateach end of the leucine rich repeats are also required for Nogo-66binding, presumably these are necessary to generate appropriate leucinerich repeat conformation.

Example 13—Blockade of Nogo by Soluble NgR Ectodomain Protein

One method for blocking a signal transduction cascade initiated byNogo-66 binding to the NgR is to provide excess soluble ectodomain ofthe receptor. A secreted fragment of the NgR protein has been producedin HEK293T cells. The cDNA encoding amino acid residues 1-348 of themurine NgR were ligated into a eukaryotic expression vector and that DNAwas transfected into HEK293T cells. Conditioned medium from these cellscontains high levels of this NgR fragment (NgR-ecto), as demonstrated byimmunoblots with an anti-NgR antibody. The conditioned medium containsapproximately 1 mg of NgR-ecto protein per liter. In the AP-Nogo bindingassay to COS-7 cells expressing full length NgR or to dorsal rootganglion neurons, the addition of NgR-ecto conditioned medium reducesthe binding of 0.5 nM AP-Nogo-66 by 80%. Complex formation betweensoluble NgR-ecto and Nogo-66 prevents binding to cell surface receptors.

For some receptor systems, such soluble receptor ligand complexes canblock signaling by creating an ineffective interaction. For example, thesoluble ectodomain of Trk serves to block neurotrophin signaling and hasbeen extensively used for this purpose (Shelton et al., (1995) J.Neurosci. 15, 477-491). Alternatively, the Nogo-66/NgR-ecto solublecomplex may bind to and stimulate the presumed second transmembrane NgRsubunit. There is precedence for this type of effect from studies ofGDNF family receptors (Cacalano et al., (1998) Neuron 21, 53-62). TheNogo-66/NgR-ecto complex does not cause growth cone collapse in thoseneurons (chick E7 retinal ganglion cells) which lack the Nogo-66receptor but containing other components of the Nogo signaling pathway.This indicates that NgR-ecto functions as a blocker of Nogo-66signaling. In direct tests, the NgR-ecto protein protects axons from theinhibitory effects of Nogo-66. NgR-ecto prevents Nogo-66-induced growthcone collapse and blocks Nogo-66-induced inhibition of neurite outgrowthfrom chick E13 DRG neurons (FIG. 12B). Furthermore, the presence ofNgR-ecto protein blocks the ability of CNS myelin to inhibit axonaloutgrowth in vitro (FIG. 12C). These data demonstrate that a NgR-ectoprotein can promote axonal regeneration in vivo.

Example 14—Regions in the Luminal/Extracellular Domain of Nogo Necessaryfor NgR Binding

Portions of the luminal/extracellular domain of Nogo were tested todetermine the amino acid sequences responsible for conveying inhibitoryactivity. To accomplish this, five 25 residue peptides, consisting ofoverlapping segments of the luminal/extracellular sequence fused to APwere constructed for testing in binding, growth cone collapse andneurite outgrowth assays.

To generate AP-fusion proteins, PCR from cDNA of human Nogo-A was usedto obtain inserts encoding residues #1055-1094, 1055-1089, 1055-1084,1055-1079, 1060-1094, 1065-1094 or 1070-1094 of hNogoA (designated 1-40,1-35, 1-30, 1-25, 6-40, 11-40, 16-40 in FIG. 5A). See FIG. 13a for theamino acid sequence of each. The inserts were excised and subcloned intothe mammalian expression vector pcAP-6. Approximately 60 hours afterconstructs were transfected into 293T cells, conditioned medium wascollected. The concentration of soluble AP-fused proteins within theconditioned medium or the presence of AP-fusion proteins within theconditioned medium from these cells was verified by measuring APactivity with the substrate p-nitro-phenyl phosphate, pNPP, or bywestern, respectively.

To determine if AP-fused deletion mutants of Nogo-66 bind mouse NgR(“mNgR”), COS-7 cells were transfected with a plasmid encoding the mouseNgR sequence ligated into pcDNA3.1. 48 hours after transfection, cellswere washed with HBH (Hanks balanced salt solution containing 20 mMsodium Hepes, pH 7.05, and 1 mg ml⁻¹ bovine serum albumin) and thenincubated with condition medium containing one of the AP-fusion proteinsdescribed above for 2 hours at 37° C. Cells were then washed, fixed, andleft in HBH at 67° C. for 14-16 h to inactivate endogenous AP. AP-fusionprotein binding to NgR expressing COS-7 cells was detected with thesubstrates NBT and BCIP (FIG. 13B).

Using this assay, AP fused Nogo-66 has been shown to bind COS7 cellsexpressing NgR with a K_(d) of approximately 7 nM. Equally high affinitybinding to NgR expressing cells, but not to non-transfected cells, wasobtained with an AP-fusion protein consisting of residues 1-40 of theNogo-66 sequence (designated 140-AP in FIG. 14A).

FIG. 14B graphically depicts the binding of 140-AP to COS-7 cellsexpressing mNgR as measured as a function of 140-AP concentration. Aplot of the bound/free versus free 140-AP indicates that the Kd of140-AP binding to mNgR in this assay is 8 nM. See FIG. 14 c.

AP-fusion proteins 1-35 and 6-40 also demonstrated binding to mNgRtransfected cells (FIG. 13B). Application of AP to these cells does notresult in any detectable binding indicating that binding is the resultof the Nogo-66 derived residues that were tested. Subsequent experiments(data not shown) have demonstrated that peptides having residues 1-35and 1-34 bind strongly and almost equivalently to mNgR, whereas peptideshaving residues 1-33 bound mNgR approximately 50% less compared to thestrong binders. Peptides having residues 1-31 and 1-30 exhibited almostno binding to NgR. Further, peptides having residues 2-40 of thehNogoA(#1055-1120) bound mNgR well whereas peptides having residues10-40 had no binding and peptides having 6-40 had intermediate binding.Taken together, the data indicates that there are two regions of thehNogoA(#1055-1120) sequence that contain residues necessary forbinding:residues 2-10 and 31-34, i.e., sequences IYKGVIQAI (SEQ IDNO:56) and EELV (SEQ ID NO:57).

Example 15—Activity of Fragments of the Luminal/Extracellular Domain ofNogo

Tests were conducted to determine if the NgR binding observed withvarious fragments of the luminal/extracellular domain of Nogo wascorrelated with inhibitory activity. E12 chick DRG growth cone collapseand neurite outgrowth assays that have been described previously wereused to determine the inhibitory activity of the fragments.

Briefly, for growth cone collapse, DRG explants were plated on plasticchamber slides precoated with 100 μg ml⁻¹ poly-_(L)-lysine and 10 μgml⁻¹ laminin. Cultures were grown 14-16 h prior to treatment.

For neurite outgrowth assays, plastic chamber slides were coated with100 μg ml⁻¹ poly-_(L)-lysine, washed, and dried. 3 μl drops of PBScontaining GST-Nogo-66 were spotted and dried. Slides were then rinsedand coated with 10 μg ml fs24⁻¹ laminin before addition of dissociatedE12 chick DRGs. AP-fusion proteins were added at the time of cellplating. Cultures were grown for 5-7 h after which neurite outgrowth wasassessed.

Out of the AP fusion proteins that bind NgR, only the AP fusion proteinscontaining residues #1085-1109 of hNogoA were active in these assays(data not shown) thus indicating that residues within this region arecritical to the inhibitory activity of the luminal/extracellular domainof Nogo. However, the activity of the AP fusion protein containingresidues #1085-1109 of hNogoA was considerably less than the larger#1055-1120 fragment. These findings indicate that regions outside ofresidues #1085-1109, but within residues #1055-1120 of hNogoA may becrucial for high affinity binding of the residues #1055-1120 of hNogoAto NgR.

To determine the activity of AP-fusion proteins of Example 14,conditioned medium containing AP-fusion proteins were added to culturesat a final concentration of 20 nM. FIGS. 15A and B show that AP fused toresidues #1055-1120 of NogoA is a potent growth-cone-collapsing agent(designated AP-Ng-66 in FIG. 15A and 1-66 in FIG. 15B). Other AP-fusionproteins containing residues #1055-1094, 1055-1089 or 1060-1094(designated as 1-40, 1-35 or 6-40, respectively in FIG. 15B) did notinduce growth cone collapse in this assay.

Although these fusion proteins bind to COS7 cells expressing NgR withhigh affinity, they fail to induce significant growth cone collapse inE12 chick DRG explant cultures. These peptides exhibit a desirablecharacteristic for blockers of Nogo activity—i.e., they themselves donot have inhibitory activity. The fusion of AP with residues #1055-1094of hNogoA is a good example of a fusion protein that binds with highaffinity to COS7 cells expressing NgR, but fails to mediate growth conecollapse. Taken together, these data suggest that high affinity bindingto NgR can be dissociated from activation of an inhibitory signalthrough NgR.

Example 16—Synthetic Peptide 140 is an Antagonist Against Nogo-66Activity

(a) Growth Cone Collapse

For further testing, a synthetic peptide containing amino acid residues#1055-1094 of hNgR, acetylated at the carboxy terminus and amidated atthe amino terminus was used [hereinafter “Peptide 140”]. As was shownwith the AP-fused version of this peptide, application of Peptide 140does not induce significant growth cone collapse in E12 chick DRGexplant cultures. Antagonist of Nogo-66 inhibitory activity may act bycompeting for, and thereby blocking NgR binding sites. To determine theantagonistic activity of Peptide 140, the above synthetic form of thepeptide was added to E12 chick DRG explant cultures approximately 10 minbefore application of various concentrations of GST-NogoA (residues#1055-1120), TPA or Sema3A. 30 min later, cultures were fixed and growthcone collapse was assessed following staining with rhodamine-phalloidin.See FIG. 16 a.

In this assay, Peptide 140 significantly blocks growth cone collapseinduced by residues #1055-1120 fused to GST. Importantly, when Peptide140 is applied to these cultures in conjunction with other growth conecollapsing agents, TPA or Sema3A, there is no significant reduction incollapse. These findings indicate that the antagonistic activity ofPeptide 140 is selective for Nogo inhibitory activity. See FIGS. 16b -d.

(b) Neurite Outgrowth Activity

Peptide 140 was tested for its ability to neutralize neurite outgrowthinhibition caused by the addition of GST fused to residues #1055-1120 ofhNogoA (designated Nogo-66 in FIG. 16e ). Plastic chamber slides werecoated with 100 μg ml⁻¹ poly-_(L)-lysine, washed, and dried. 3 μl dropsof PBS containing GST-hNogoA(residues #1055-1120) were spotted anddried. Slides were then rinsed and coated with 10 μg ml fs24⁻¹ lamininbefore addition of dissociated E12 chick DRGs. Peptide 140 was added atthe time of cell plating. Cultures were grown for 5-7 h after whichneurite outgrowth was assessed.

While GST-hNogoA(residues #1055-1120) dramatically reduces growth inthese cultures, application of Peptide 140 alone has no observableeffect on neurite outgrowth from these cells. See FIG. 16e . However,when cells are grown in the presence of both Peptide 140 andGST-hNogoA(residues #1055-1120), extensive outgrowth is observed.Importantly, challenging GST-hNogoA(residues #1055-1120)-inducedactivity with a scrambled version of Peptide 140[acetyl-SYVKEYAPIFAGKSRGEIKYQSIEIHEAQVRSDELVQSLN-amide] does not resultin blockade of outgrowth inhibition. Taken together, these studiessuggest that Peptide 140 can be used as a functional antagonist ofinhibitory activity of the luminal/extracellular domain of Nogo. SeeFIG. 16 e.

Example 17—Peptide 140 can Neutralize the Inhibitory Activity of CNSMyelin at Low Concentrations, but not High Concentrations of CNS Myelin

Inhibitory molecules associated with CNS myelin include MAG, chondroitinsulfate proteoglycans, and Nogo. Currently, the relative contribution ofeach of these molecules to the non-permissiveness of CNS myelin islargely unknown. To this end, standard in vitro assays were used todetermine whether Peptide 140 can neutralize the inhibitory activity ofCNS myelin (FIG. 17).

To determine the antagonistic activity of Peptide 140 against CNSmyelin, the above synthetic peptide was added approximately 10 minbefore application of CNS myelin. 30 min later, cultures were fixed andgrowth cone collapse was assessed following staining withrhodamine-phalloidin. For neurite outgrowth assays, plastic chamberslide were coated with 100 μg ml⁻¹ poly-_(L)-lysine, washed, and dried.3 μl drops of PBS containing CNS myelin were spotted and dried. Slideswere then rinsed and coated with 10 μg ml fs24⁻¹ laminin before additionof dissociated E12 chick DRGs. Peptide 140, or the scrambled version ofPeptide 140, was added at the time of cell plating. Cultures were grownfor 5-7 h after which neurite outgrowth was assessed.

When applied to E12 chick DRG explant cultures, purified CNS myelinpotently mediates growth cone collapse. The addition of both Peptide 140and CNS myelin to these cultures reveals that at higher concentrationsof myelin, the peptide had no effect on inhibitory activity. This resultwas not necessarily unexpected given that CNS myelin is known to containinhibitory molecules other than Nogo. However, at the lowest myelinconcentrations tested, Peptide 140 reduces myelin induced growth conecollapse to control levels. These data suggest that Nogo may be the onlyactive inhibitor at low concentrations of myelin (and may therefore bethe most potent inhibitor present in CNS myelin).

In addition to mediating growth cone collapse, CNS myelin dramaticallyreduces neurite outgrowth when applied to dissociated E12 chick DRGcultures. Addition of Peptide 140 to these cultures results in a partialneutralization of this inhibitory activity when CNS myelin is presentedas a bound inhibitor (FIG. 17). For example, neurite outgrowth on a 20ng spot of myelin increases from 35% to 65% (as compared with controloutgrowth) following treatment with Peptide 140. Maximal activity ofPeptide 140 is obtained at approximately 250 nM and is progressivelylost with higher dilutions of the peptide. The scrambled version ofPeptide 140 is ineffective at blocking CNS myelin induced neuriteoutgrowth inhibition. Taken together, these data suggest that Nogo is animportant contributor to the inhibitory activity of CNS myelin. Further,much of the activity of Nogo-A may be attributable to the Nogo-66inhibitory domain.

Peptide 140 significantly reduces myelin induced growth cone collapseand can partially restore neurite outgrowth in cultures grown on boundCNS myelin. Thus, Nogo can be a potent inhibitory molecule in CNSmyelin.

There has been reports that neutralization of Nogo activity with themonoclonal antibody IN-1, raised against a myelin fraction enriched inNogo-A, can partially block the inhibitory activity of CNS myelin bothin vitro and in vivo. However, interpretation of the results of thesestudies is complicated by the presence of two inhibitory domains inNogo-A (at residues #1055-1120 and the N-terminus of hNogoA) and a lackof information regarding the epitope of Nogo-A recognized by the IN-1antibody. Further, using IN-1 to probe a Western blot of proteinsextracted from spinal cord reveals binding to Nogo-A but also to anumber of other unidentified protein species indicating that theantibody is not highly selective for Nogo-A. In contrast, a peptidesderived from the luminal/extracellular domain of Nogo according to thisinvention selectively block hNogoA activity.

Example 18—NgR LRR Domains are Required for Binding to Nogo

To define residues critical for binding to Nogo-66 [hereinafter,hNogo-A(1055-1120)], mouse NgR (hereinafter mNgR) deletion mutants weregenerated and tested for their ability to bind hNogo-A(1055-1120). Theamino acid sequence of mNgR contains a signal sequence, anamino-terminal region (NT), eight leucine-rich repeat (LRR) domains (LRR1-8), a LRR carboxy-terminal domain (LRRCT), a unique carboxy terminaldomain (CT), and a GPI anchor domain. A series of mNgR mutant proteinswith specific regions deleted was created using PCR-based site-directedmutagenesis (FIG. 1A).

The mNgR (WTNgR) and mNgR deletion mutants were ligated into the vectorpSecTag2Hygro (Invitrogen, Buringame, Calif.). The vector adds to eachof the proteins a secretion signal, a C-terminal polyhistidine (6×His)tag, and a C-terminal epitope recognized by the anti-His (C-term)antibody. wtNgR encodes residues 1 to 473 of mNgR (Fournier et al.,Nature 409:341-346, 2001).

The Ng_(Δ)RNT construct encodes residues 58 to 473 of mNgR. TheNgR_(Δ)NT construct was made by using the primers _(Δ)LRR-NT5(5′-tgggatccgaacaaaaactcatctcagaagaggatctgtctagccagcgaatcttcctgcatggc-3′)and NgR3X (5′-ttctcgaggtcagcagggcccaagcactgtcc-3′) to amplify a sequencefrom the wtNgR-pSecTag2Hygro plasmid. The amplified sequence was ligatedinto the XhoI/BamHI of pSecTag2.

The NgLRR-construct encodes residues 306 to 473 of mNgR. The NgLRRconstruct was made by using the primers, MycNgR305(5′-tgggatccgaacaaaaactcatctcagaagaggatctgctagagggctgtgctgtggcttca-3′)and NgR3X (above) to amplify a sequence from the from thewtNgR-pSecTag2Hygro plasmid. The amplified sequence was ligated into theXhoI/BamHI of pSecTag2.

The NgR_(Δ)CT contruct encodes residues 26 to 305 and 443 to 473 ofmNgR, thereby including the LRR and GPI regions of mNgR. Primers MycNgR(tgggatccgaacaaaaactcatctcagaagaggatctgccatgccctggtgcttgtgtgtgct) and2NgRt313 (ttgcggccgctgaagccacagcacagccctctag) were used to amplify asequence from the wtNgR-pSecTag2Hygro plasmid. Primers TM/GPI5(5′-ttgcggccgctgagggttcaggggctctgcctgct-3′) and NgR3X (above) were usedto amplify a sequence from the wtNgR-pSecTag2Hygro plasmid. Theamplified sequences were ligated together at the NotI site and thenligated into the BamHI/XhoI sites of pSecTag2.

The mNgR LLR deletions and NgR_(Δ)LRRCT deletion mutants were generatedusing ExSite™ PCR-based site-directed mutagenesis kit (Stratagene, LaJolla, Calif.). Generally, the primers described below were used toamplify a sequence from the wtNgR pSecTag2 plasmid. The ends of theamplified products were ligated together. The resulting constructs weretransfected into COS-7 cells.

The NgR_(Δ)1-2 construct encodes residues 1 to 56 and residues 106 to473 of mNgR. The primers used for making the NgR_(Δ)1-2 construct wereDEL LRR (5′PO4) (5′-ggctgggatgccagtgggcacagc-3′) and DEL LRR2(5′-ctcctggagcaactagatcttagt-3′). The NgR_(Δ)3-4 construct encodesresidues 1 to 105 and residues 155 to 473 of mNgR. The primers used formaking the NgR_(Δ)3-4 constructs were DEL LRR3 (5′PO4)(5′-ggtcagaccagtgaaggcagcagc-3′) and DEL LRR4(5′-gctctgcagtacctctacctacaa-3′). The NgR_(Δ)5-6 construct encodesresidues 1 to 153 and residues 203 to 473 of mNgR. The primers used formaking the NgR_(Δ)5-6 construct were DEL LRR5 (5′PO4)(5′-tgctagtccacggaataggccggg-3′) and DEL LRR6 (5′PO4)(5′-agtcttgaccgcctcctcttgcac-3′). The NgR_(Δ)7-8 construct encodesresidues 1 to 202 and residues 251 to 473 of mNgR. The primers used tomake the NgR_(Δ)7-8 construct were DEL LRR7 (5′PO4)(5′-gtgcaggccacggaaagcgtgctc-3′) and DEL LRR8(5′-tctctgcagtacctgcgactcaat-3′). The NgR_(Δ)LRRCT construct encodesresidues 1 to 259 and residues 311 to 473 of mNgR. The primers used tomake the NgR_(Δ)LRRCT construct were 3DLRR CT(5′-gtggcttcaggacccttccgtcccatc-3′) and 5 DLRRCT (5′ PO4)(5′-gtcattgagtcgcaggtactgcagagacct-3′). Expression of the mNgR mutantsin COS-7 cells was verified by SDS-PAGE and immunoblotting (data notshown).

A vector encoding AP-hNogo-A(1055-1120) was constructed as described inFournier et al., supra). The vector encoding AP-NgR was made by ligatingthe mNgR coding sequence from residues 27-451 in frame with the signalsequence-6×His-placental alkaline phosphatase (AP) sequence of thevector known as pAP-6 (Nakamura et al., Neuron 2: 1093-1100, 1988).

AP-hNogo-A(1055-1120) was prepared by transfecting the expressionplasmid into HEK293T cells and, after four days, collecting theconditioned medium and purifying the secreted AP-hNogo-A(155-1120)protein by Ni2+ affinity chromatography as described (Nakamura et al.,supra).

To determine whether mNgR or mNgR deletion mutants bound tohNogo-A(1055-1120), wtNgR or mNgR deletion mutants were transfected intoCOS-7 cells. Forty-eight hours after the transfection, the transfectedCOS-7 cells were washed with hanks balanced salt solution containing 20mM sodium HEPES, pH 7.05, and 1 mg/ml bovine serum albumin (BSA)[hereinafter “HBH”]. Cells were then incubated for 2 hours at 23° C.with a conditioned medium enriched with purified AP-hNogo-A(1055-1120)diluted in HBH. AP-fusion protein was detected as previously describedfor AP-Sema3A (Takahashi et al., Nature Neurosci. 1:487-493, 1998).

wtNgR and NgRΔCT transfected COS-7 cells bound to AP-hNogo-A(1055-1120),but the other deletion mutants did not (FIG. 18B). TheAP-hNogo-A(1055-1120) binding pattern indicates that multiple residueswithin the NgR LRR region are required for AP-Nogo binding. Because theNgRΔ1-2, NgRΔ3-4, NgRΔ5-6, and NgRΔ7-8 deletions remove entire LRRdomains it is unlikely that the entire tertiary structure of mNgR isdisrupted.

Example 19—The Effect of NgRCT on Mediating NgR-Dependent Inhibition

Because the mouse NgRCT domain was determined to be dispensable forhNogo-A(1055-1120) binding, the ability of NgRΔCT to mediateNogo-dependent inhibition was examined. HSVNgR constructs transfectedinto HEK293T cells mediated the expression of mNgR proteins of thepredicted molecular weight, as determined by SDS-PAGE and anti-Myc andanti-NgR immunoblotting (FIG. 19A). Day E7 chick retinal ganglion cells(RGCs) were grown for 12 hr, then further incubated for 24 hr withHSVNgR preparations. Explants were fixed with 4% paraformaldehyde with0.1 M PO₄ and 20% sucrose and stained with phalloidin or with anti-mycantibodies. HSVNgR protein expression was detected in axons of infected(RGC) cultures (FIG. 19B).

Growth cone collapse in response to GST-hNogo-A(1055-1120) wasinvestigated in infected RGC cultures. Retinal explants infected withrecombinant viral preparations of PlexinA1 (PlexA1), wild-type NgR(wtNgR), NgRL1 chimeric receptor in which the GPI domain has beenreplaced by the transmembrane region and cytoplasmic tail from the mouseadhesion protein L1 (NgRL1), or NgR carboxy terminal deletion mutant(NgRΔCT) for 12 hr. Following infection, the cells were treated for 30min with 0, 50, 250, or 500 nM GST-hNogo-A(1055-1120) (GrandPre et al.,Nature 403: 439-444, 2000), fixed with 4% paraformaldehyde with 0.1 MPO₄ and 20% sucrose, and stained with phalloidin. As shown in FIG. 20,cells infected with the control PlexA1 virus did not respond toGST-hNogo-A(1055-1120), whereas cells infected with wtNgR underwentgrowth cone collapse in response to GST-hNogo-A(1055-1120). Cellsinfected with NgRΔCT were insensitive to GST-hNogo-A(1055-1120). The CTregion of NgR is therefore required for effective NgR inhibitorysignaling.

Example 20—The Effect of the CT Domain Alone on NgR Inhibitory Signaling

As NgR is a GPI linked protein tethered to the plasma membrane, it islikely that a second protein exists in a NgR signaling complex that isresponsible for transducing Nogo signals within the cell. Onepossibility is that the CT domain of NgR may bind to a transducingcomponent and initiate an intracellular signaling cascade upon ligandbinding. This possibility would be consistent with the signalingincompetence of NgRΔCT. If so, it is also possible that the NgR CTregion may be capable of constitutive inhibitory activity. To test thispossibility, a GSTNgRCT fusion protein was produced by PCR amplifyingthe CT region of NgR (amino acids 310-450) and ligating the fragmentinto the BamHI/EcoRI site of pGEX2T. The fusion protein was expressedand tested in a neurite outgrowth assay. E13 chick dorsal root ganglion(DRG) cells were dissociated and plated in the presence or absence of100 nM soluble GSTNgRCT and assayed for neurite outgrowth lengths. Inthis assay, GST-hNogo-A(1055-1120) has been shown to inhibit neuriteoutgrowth (Fournier et al., supra). Soluble GSTNgRCT did not alterneurite outgrowth lengths, nor did it attenuate or enhance the responseof dissociated E13 DRGs to GST-hNogo-A(1055-1120) substrates (FIG. 21).

Example 21—The NgR GPI Domain is not Required for NgR Signaling

To test the possibility that the GPI anchor has a role in mediatinginhibitory Nogo signaling, a chimeric NgR molecule was constructed andassessed for its ability to correctly localize within the cell. HSVL1NgRcontains a HSVNgR fusion in which the NgR GPI domain is replaced withthe transmembrane domain of L1. HEK293T cells were cultured in 6-mmdishes and transfected with HSVwtNgR or HSVL1NgR. After 48 hr, cellswere rinsed with PBS and lysed on ice with 375 μl precooled buffercontaining 50 mM Tris-HCl (pH 7.4), 150 mM NaCl, 5 mM EDTA, and 0.1%Triton X-100, (hereinafter “TNEX”), and 10 mM NaF and a proteaseinhibitor cocktail (Roche Diagnostics, Mannheim, Germany). Cells werehomogenized by passing the ice-cold lysates through a 27 G needle 10times. Extracts were adjusted to 35% OptiPrep (Gibco BRL) by adding 525μl of 60% OptiPrep/0.1% Triton X-100, then placed in an ultracentrifugetube and overlayed with 8.75 ml of 30% OptiPrep in TNEX and 1 ml ofTNEX. After centrifugation (4 hr, 200,000×g, 4° C.), seven fractionswere collected, precipitated with trichloroacetic acid, washed withacetone, air dried, and resuspended in Laemlli sample buffer. Fractionswere analyzed by 8% SDS-PAGE and immunoblotting with the NgR antibody(Fournier et al., supra). Transferrin receptor (TfR) was detected withan anti-TfR monoclonal antibody; caveolin was detected withanti-caveolin rabbit polyclonal antibody.

As expected for a GPI-anchored protein, wtNgR localized mainly tocaveolin-rich lipid raft fractions (FIG. 22). A much smaller proportionof the chimeric L1NgR was localized to the lipid raft fraction.Expression of the wild-type HSVNgR or HSVNgRL1 chimeric protein inHEK293T cells results in an altered distribution of HSVNgRL1.

Example 22—mNgR Binds mNgR

NgR was tested for the ability to self-associate. For this study, mNgR[hereinafter, wtNgR or WT] and mNgR deletion mutants (see FIG. 18A) weretransfected into COS-7 cells. Forty-eight hours after the transfection,the transfected COS-7 cells were washed with HBH. Cells were thenincubated for 2 hours at 23° C. with a conditioned medium containingAP-hNogo-A(1055-1120) fusion protein diluted in HBH. AP-fusion proteinwas detected as previously described for AP-Sema3A (Takahashi et al.,Nature Neurosci. 1:487-493, 1998). Similar to the AP-Nogo bindingprofile, AP-NgR bound to wtNgR and NgRΔCT (FIG. 23). Nogo treatment hadlittle, if any, effect on the NgR-NgR interaction (data not shown).Other NgR deletion mutants did not bind AP-NgR. The same NgR domains arerequired for GST-hNogo-A(1055-1120) binding and NgR oligomerization

Example 23—Soluble NgR Antagonizes Nogo and Myelin-Dependent Inhibition

Although the role of the GPI anchor may be to regulate NgR cellularcompartmentalization, another possible role for the GPI linkage is toprovide a NgR cleavage site. Cleaving NgR could serve to affecthNogo-A(1055-1120) signaling by rendering a neuron insensitive tohNogo-A(1055-1120) and by releasing soluble NgR that could then act onadjacent cells to modulate hNogo-A(1055-1120) signaling. To determine ifsoluble mNgR modulates hNogo-A(1055-1120)-dependent inhibition, asoluble mNgR was generated by inserting a truncated cDNA encoding mNgRresidues 1-348 in frame with a myc-His carboxy tag into pcDNA3.1. Theresulting plasmid expressing mNgREcto was transfected into HEK293Tcells, and conditioned media containing mNgREcto protein was collected.To test the effect of mNgREcto on Nogo signaling, E13 dissociated DRGswere plated in the presence of hNogo-A(1055-1120) or myelin. Theinhibitors were presented in either soluble or substrate-bound forms.For neurite outgrowth assays on hNogo-A(1055-1120) or myelin substrates,Permanox chamber slides were coated with 100μ, fs24 g ml⁻¹poly-L-Lysine, washed, and then 3-μl drops of phosphate-buffered saline(hereinafter “PBS”) containing 0, 10, 50, or 150 ng ofGST-hNogo-A(1055-1120) or myelin were spotted and dried.GST-hNogo-A(1055-1120) and myelin were prepared as previously described(GrandPre et al., supra; Fournier et al., J. Cell Biol. 149:411-421,2000). After three PBS washes, slides were coated with 10 μg ml⁻¹laminin. Laminin was then aspirated and dissociated E13 chick DRGneurons were added. After 6-8 hr of outgrowth, cultures were fixed andneurite outgrowth lengths were assessed. For blockade experiments withNgREcto, spots were incubated with HEK293T cell conditioned media orNgREcto-transfected-HEK293T cell conditioned media following for 1 hrfollowing the laminin coating step and before the addition ofdissociated neurons. As shown in FIG. 24, following blockage withNgREcto, neurite outgrowth inhibition by Nogo or myelin substrates waspartially reversed. Thus, soluble fragments of NgR might servephysiologically or pharmacologically to reduce GST-hNogo-A(1055-1120)inhibition of axonal regeneration.

To test the signaling capability of NgRLI, recombinant HSVL1NgRpreparations were produced and used to infect E7 RGCs. Infected RGCswere treated with GST-hNogo-A(1055-1120) and growth cone collapse wasassessed (FIG. 20). At high concentrations of GST-hNogo-A(1055-1120),NgRL1 transduces Nogo signals as efficiently as wtNgR. However, at 50 nMGST-hNogo-A(1055-1120), wtNgR is capable of signaling whereas NgRL1infected RGCs are not responsive to GST-hNogo-A(1055-1120). Thisindicates that NgRL1 is capable of mediating inhibitory signals inresponse to Nogo, however less efficiently than wtNgR. When transfectedHEK293T cells were treated with GST-hNogo-A(1055-1120), the membranefractionation profile of wtNgR and L1Ngr remained the same (data notshown) suggesting that Nogo does not modulate NgR localization to lipidraft compartments in HEK293T cells. It is however possible that ligandbinding to NgR modifies signaling within the compartment as is the casefor ephrins (Davy et al., Genes Dev., 13:3125-3135, 1999) or recruitsunknown signaling partners to a lipid raft complex. Because theintracellular signals induced by Nogo have not been elucidated, itremains to be determined if ligand binding effects signaling events atcaveolar microdomains.

Throughout the specification, the word “comprise,” or variations such as“comprises” or “comprising,” will be understood to imply the inclusionof a stated integer or group of integers but not the exclusion of anyother integer or group of integers.

Although the present invention has been described in detail withreference to examples above, it is understood that various modificationscan be made without departing from the spirit of the invention.Therefore, it will be appreciated that the scope of this invention isencompassed by the embodiments of the inventions recited herein and thespecification rather than the specific examples which are exemplifiedbelow. All cited patents and publications referred to in thisapplication are herein incorporated by reference in their entirety. Theresults of part of the experiments disclosed herein have been published(GrandPré et al., (2000) Nature 403, 439-444) after the filing date ofU.S. Provisional Application 60/175,707 from which this applicationclaims priority, this publication herein incorporated by reference inits entirety.

What is claimed:
 1. A method of inhibiting CNS myelin-mediated neuriteoutgrowth inhibition or promoting axonal regeneration comprisingcontacting a neuron with a Nogo receptor (NgR) antagonist selected fromthe group consisting of: (a) an isolated NgR polypeptide; and (b) anantibody or antigen binding fragment thereof that binds an NgRpolypeptide; wherein said NgR antagonist inhibits CNS myelin-inducedneurite outgrowth inhibition or promotes axonal regeneration.
 2. Amethod of promoting neurite outgrowth or axonal regeneration in a mammalcomprising administering to a mammal in need thereof an effective amountof a Nogo receptor (NgR) antagonist, wherein said NgR antagonist isselected from the group consisting of: (a) an isolated NgR polypeptide;and (b) an antibody or antigen binding fragment thereof that binds anNgR polypeptide; wherein said NgR antagonist inhibits CNS myelin-inducedneurite outgrowth inhibition or promotes axonal regeneration.
 3. Amethod of treating a central nervous system disease, disorder or injuryin a mammal, comprising administering to a mammal in need thereof aneffective amount of an NgR antagonist selected from the group consistingof: (a) an isolated NgR polypeptide; and (b) an antibody or antigenbinding fragment thereof that binds an NgR polypeptide; wherein said NgRantagonist inhibits CNS myelin-induced neurite outgrowth inhibition orpromotes axonal regeneration.
 4. The method of claim 3, wherein saidcentral nervous system disease, disorder or injury is selected from thegroup consisting of cranial or cerebral trauma, spinal cord injury,stroke, multiple sclerosis, monophasic demyelination, encephalomyelitis,multifocal leukoencephalopathy, panencephalitis, Marchiafava-Bignamidisease, pontine myelinolysis, adrenoleukodystrophy,Pelizaeus-Merzbacher disease, Spongy degeneration, Alexander's disease,Canavan's disease, metachromatic leukodystrophy, and Krabbe's disease.5. An isolated polynucleotide comprising a first nucleic acid encoding afragment of the polypeptide of SEQ ID NO:2, or a variant thereof,wherein said polypeptide inhibits NOGO-receptor-mediated neuriteoutgrowth inhibition.
 6. The polynucleotide of claim 5, wherein saidpolypeptide is selected from the group consisting of: (a) amino acids27-309 of SEQ ID NO:2; (b) amino acids 27-445 of SEQ ID NO:2; (c) aminoacids 1-348 of SEQ ID NO:2; and (d) amino acids 1-309 of SEQ ID NO:2. 7.The polynucleotide of claim 6, further comprising a second nucleic acidencoding a heterologous polypeptide fused to said polypeptide.
 8. Avector comprising the polynucleotide of claim
 5. 9. The vector of claim8, wherein said polynucleotide is operably linked to one or moreexpression control elements.
 10. An isolated host cell comprising thepolynucleotide of claim
 5. 11. The host cell of claim 10, wherein saidpolynucleotide is operably linked to one or more expression controlelements.
 12. A method for producing a polypeptide comprising culturingthe host cell of claim 10 under conditions suitable for expression ofthe polypeptide and recovering the polypeptide from the culture medium.13. A composition comprising a polypeptide encoded by the polynucleotideof claim 5 and a pharmaceutically acceptable carrier.